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diff --git a/python-macs2.spec b/python-macs2.spec new file mode 100644 index 0000000..8f89c9f --- /dev/null +++ b/python-macs2.spec @@ -0,0 +1,1068 @@ +%global _empty_manifest_terminate_build 0 +Name: python-MACS2 +Version: 2.2.7.1 +Release: 1 +Summary: Model Based Analysis for ChIP-Seq data +License: BSD License +URL: http://github.com/taoliu/MACS/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/e2/61/85d30ecdd34525113e28cb0c5a9f393f93578165f8d848be5925c0208dfb/MACS2-2.2.7.1.tar.gz +BuildArch: noarch + + +%description +`callpeak` | Main MACS2 Function to call peaks from alignment results. +`bdgpeakcall` | Call peaks from bedGraph output. +`bdgbroadcall` | Call broad peaks from bedGraph output. +`bdgcmp` | Comparing two signal tracks in bedGraph format. +`bdgopt` | Operate the score column of bedGraph file. +`cmbreps` | Combine BEDGraphs of scores from replicates. +`bdgdiff` | Differential peak detection based on paired four bedGraph files. +`filterdup` | Remove duplicate reads, then save in BED/BEDPE format. +`predictd` | Predict d or fragment size from alignment results. +`pileup` | Pileup aligned reads (single-end) or fragments (paired-end) +`randsample` | Randomly choose a number/percentage of total reads. +`refinepeak` | Take raw reads alignment, refine peak summits. +We only cover `callpeak` subcommand in this document. Please use +`macs2 COMMAND -h` to see the detail description for each option of +each subcommand. +### Call peaks +This is the main function in MACS2. It can be invoked by `macs2 +callpeak` . If you type this command with `-h`, you will see a full +description of command-line options. Here we only list the essentials. +#### Essential Options +##### `-t`/`--treatment FILENAME` +This is the only REQUIRED parameter for MACS. The file can be in any +supported format -- see detail in the `--format` option. If you have +more than one alignment file, you can specify them as `-t A B C`. MACS +will pool up all these files together. +##### `-c`/`--control` +The control, genomic input or mock IP data file. Please follow the +same direction as for `-t`/`--treatment`. +##### `-n`/`--name` +The name string of the experiment. MACS will use this string NAME to +create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`, +`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So +please avoid any confliction between these filenames and your existing +files. +##### `--outdir` +MACS2 will save all output files into the specified folder for this +option. A new folder will be created if necessary. +##### `-f`/`--format FORMAT` +Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`, +`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which +will allow MACS to decide the format automatically. `AUTO` is also +useful when you combine different formats of files. Note that MACS +can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to +implicitly specify the format for `BAMPE` and `BEDPE`. +Nowadays, the most common formats are `BED` or `BAM` (including +`BEDPE` and `BAMPE`). Our recommendation is to convert your data to +`BED` or `BAM` first. +Also, MACS2 can detect and read gzipped file. For example, `.bed.gz` +file can be directly used without being uncompressed with `--format +BED`. +Here are detailed explanation of the recommanded formats: +###### `BED` +The BED format can be found at [UCSC genome browser +website](http://genome.ucsc.edu/FAQ/FAQformat#format1). +The essential columns in BED format input are the 1st column +`chromosome name`, the 2nd `start position`, the 3rd `end position`, +and the 6th, `strand`. +Note that, for `BED` format, the 6th column of strand information is +required by MACS. And please pay attention that the coordinates in BED +format are zero-based and half-open. See more detail at +[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1). +###### `BAM`/`SAM` +If the format is `BAM`/`SAM`, please check the definition in +(http://samtools.sourceforge.net/samtools.shtml). If the `BAM` file is +generated for paired-end data, MACS will only keep the left mate(5' +end) tag. However, when format `BAMPE` is specified, MACS will use the +real fragments inferred from alignment results for reads pileup. +###### `BEDPE` or `BAMPE` +A special mode will be triggered while the format is specified as +`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED` +files as paired-end data. Instead of building a bimodal distribution +of plus and minus strand reads to predict fragment size, MACS2 will +use actual insert sizes of pairs of reads to build fragment pileup. +The `BAMPE` format is just a `BAM` format containing paired-end alignment +information, such as those from `BWA` or `BOWTIE`. +The `BEDPE` format is a simplified and more flexible `BED` format, +which only contains the first three columns defining the chromosome +name, left and right position of the fragment from Paired-end +sequencing. Please note, this is NOT the same format used by +`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a +standard `BED` format. You can use MACS2 subcommand `randsample` to +convert a `BAM` file containing paired-end information to a `BEDPE` +format file: +``` +macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed +``` +##### `-g`/`--gsize` +PLEASE assign this parameter to fit your needs! +It's the mappable genome size or effective genome size which is +defined as the genome size which can be sequenced. Because of the +repetitive features on the chromosomes, the actual mappable genome +size will be smaller than the original size, about 90% or 70% of the +genome size. The default *hs* -- 2.7e9 is recommended for human +genome. Here are all precompiled parameters for effective genome size: + * hs: 2.7e9 + * mm: 1.87e9 + * ce: 9e7 + * dm: 1.2e8 +Users may want to use k-mer tools to simulate mapping of Xbps long +reads to target genome, and to find the ideal effective genome +size. However, usually by taking away the simple repeats and Ns from +the total genome, one can get an approximate number of effective +genome size. A slight difference in the number won't cause a big +difference of peak calls, because this number is used to estimate a +genome-wide noise level which is usually the least significant one +compared with the *local biases* modeled by MACS. +##### `-s`/`--tsize` +The size of sequencing tags. If you don't specify it, MACS will try to +use the first 10 sequences from your input treatment file to determine +the tag size. Specifying it will override the automatically determined +tag size. +##### `-q`/`--qvalue` +The q-value (minimum FDR) cutoff to call significant regions. Default +is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are +calculated from p-values using the Benjamini-Hochberg procedure. +##### `-p`/`--pvalue` +The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead +of q-value. +##### `--min-length`, `--max-gap` +These two options can be used to fine-tune the peak calling behavior +by specifying the minimum length of a called peak and the maximum +allowed a gap between two nearby regions to be merged. In other words, +a called peak has to be longer than `min-length`, and if the distance +between two nearby peaks is smaller than `max-gap` then they will be +merged as one. If they are not set, MACS2 will set the DEFAULT value +for `min-length` as the predicted fragment size `d`, and the DEFAULT +value for `max-gap` as the detected read length. Note, if you set a +`min-length` value smaller than the fragment size, it may have NO +effect on the result. For broad peak calling with `--broad` option +set, the DEFAULT `max-gap` for merging nearby stronger peaks will be +the same as narrow peak calling, and 4 times of the `max-gap` will be +used to merge nearby weaker (broad) peaks. You can also use +`--cutoff-analysis` option with the default setting, and check the +column `avelpeak` under different cutoff values to decide a reasonable +`min-length` value. +##### `--nolambda` +With this flag on, MACS will use the background lambda as local +lambda. This means MACS will not consider the local bias at peak +candidate regions. +##### `--slocal`, `--llocal` +These two parameters control which two levels of regions will be +checked around the peak regions to calculate the maximum lambda as +local lambda. By default, MACS considers 1000bp for small local +region(`--slocal`), and 10000bps for large local region(`--llocal`) +which captures the bias from a long-range effect like an open +chromatin domain. You can tweak these according to your +project. Remember that if the region is set too small, a sharp spike +in the input data may kill a significant peak. +##### `--nomodel` +While on, MACS will bypass building the shifting model. +##### `--extsize` +While `--nomodel` is set, MACS uses this parameter to extend reads in +5'->3' direction to fix-sized fragments. For example, if the size of +the binding region for your transcription factor is 200 bp, and you +want to bypass the model building by MACS, this parameter can be set +as 200. This option is only valid when `--nomodel` is set or when MACS +fails to build model and `--fix-bimodal` is on. +##### `--shift` +Note, this is NOT the legacy `--shiftsize` option which is replaced by +`--extsize`! You can set an arbitrary shift in bp here. Please Use +discretion while setting it other than the default value (0). When +`--nomodel` is set, MACS will use this value to move cutting ends (5') +then apply `--extsize` from 5' to 3' direction to extend them to +fragments. When this value is negative, ends will be moved toward +3'->5' direction, otherwise 5'->3' direction. Recommended to keep it +as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together +with `--extsize` option for detecting enriched cutting loci such as +certain DNAseI-Seq datasets. Note, you can't set values other than 0 +if the format is BAMPE or BEDPE for paired-end data. The default is 0. +Here are some examples for combining `--shift` and `--extsize`: +1. To find enriched cutting sites such as some DNAse-Seq datasets. In +this case, all 5' ends of sequenced reads should be extended in both +directions to smooth the pileup signals. If the wanted smoothing +window is 200bps, then use `--nomodel --shift -100 --extsize 200`. +2. For certain nucleosome-seq data, we need to pile up the centers of +nucleosomes using a half-nucleosome size for wavelet analysis +(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about +147bps, this option can be used: `--nomodel --shift 37 --extsize 73`. +##### `--keep-dup` +It controls the MACS behavior towards duplicate tags at the exact same +location -- the same coordination and the same strand. The default +`auto` option makes MACS calculate the maximum tags at the exact same +location based on binomial distribution using 1e-5 as p-value cutoff; +and the `all` option keeps every tag. If an integer is given, at most +this number of tags will be kept at the same location. The default is +to keep one tag at the same location. Default: 1 +##### `--broad` +When this flag is on, MACS will try to composite broad regions in +BED12 ( a gene-model-like format ) by putting nearby highly enriched +regions into a broad region with loose cutoff. The broad region is +controlled by another cutoff through `--broad-cutoff`. Please note +that, the `max-gap` value for merging nearby weaker/broad peaks is 4 +times of `max-gap` for merging nearby stronger peaks. The later one +can be controlled by `--max-gap` option, and by default it is the +average fragment/insertion length in the PE data. DEFAULT: False +##### `--broad-cutoff` +Cutoff for the broad region. This option is not available unless +`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise, +it's a q-value cutoff. DEFAULT: 0.1 +##### `--scale-to <large|small>` +When set to `large`, linearly scale the smaller dataset to the same +depth as the larger dataset. By default or being set as `small`, the +larger dataset will be scaled towards the smaller dataset. Beware, to +scale up small data would cause more false positives. +##### `-B`/`--bdg` +If this flag is on, MACS will store the fragment pileup, control +lambda in bedGraph files. The bedGraph files will be stored in the +current directory named `NAME_treat_pileup.bdg` for treatment data, +`NAME_control_lambda.bdg` for local lambda values from control. +##### `--call-summits` +MACS will now reanalyze the shape of signal profile (p or q-score +depending on the cutoff setting) to deconvolve subpeaks within each +peak called from the general procedure. It's highly recommended to +detect adjacent binding events. While used, the output subpeaks of a +big peak region will have the same peak boundaries, and different +scores and peak summit positions. +##### `--buffer-size` +MACS uses a buffer size for incrementally increasing internal array +size to store reads alignment information for each chromosome or +contig. To increase the buffer size, MACS can run faster but will +waste more memory if certain chromosome/contig only has very few +reads. In most cases, the default value 100000 works fine. However, if +there are a large number of chromosomes/contigs in your alignment and +reads per chromosome/contigs are few, it's recommended to specify a +smaller buffer size in order to decrease memory usage (but it will +take longer time to read alignment files). Minimum memory requested +for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * +8 Bytes. DEFAULT: 100000 +#### Output files +1. `NAME_peaks.xls` is a tabular file which contains information about + called peaks. You can open it in excel and sort/filter using excel + functions. Information include: + - chromosome name + - start position of peak + - end position of peak + - length of peak region + - absolute peak summit position + - pileup height at peak summit + - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then + this value should be 10) + - fold enrichment for this peak summit against random Poisson + distribution with local lambda, + - -log10(qvalue) at peak summit + Coordinates in XLS is 1-based which is different from BED + format. When `--broad` is enabled for broad peak calling, the + pileup, p-value, q-value, and fold change in the XLS file will be + the mean value across the entire peak region, since peak summit + won't be called in broad peak calling mode. +2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the + peak locations together with peak summit, p-value, and q-value. You + can load it to the UCSC genome browser. Definition of some specific + columns are: + - 5th: integer score for display. It's calculated as + `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on + whether `-p` (pvalue) or `-q` (qvalue) is used as score + cutoff. Please note that currently this value might be out of the + [0-1000] range defined in [UCSC ENCODE narrowPeak + format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You + can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by + using the following 1-liner awk: `awk -v OFS="\t" + '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak` + - 7th: fold-change at peak summit + - 8th: -log10pvalue at peak summit + - 9th: -log10qvalue at peak summit + - 10th: relative summit position to peak start + The file can be loaded directly to the UCSC genome browser. Remove + the beginning track line if you want to analyze it by other tools. +3. `NAME_summits.bed` is in BED format, which contains the peak + summits locations for every peak. The 5th column in this file is + the same as what is in the `narrowPeak` file. If you want to find + the motifs at the binding sites, this file is recommended. The file + can be loaded directly to the UCSC genome browser. Remove the + beginning track line if you want to analyze it by other tools. +4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to + `narrowPeak` file, except for missing the 10th column for + annotating peak summits. This file and the `gappedPeak` file will + only be available when `--broad` is enabled. Since in the broad + peak calling mode, the peak summit won't be called, the values in + the 5th, and 7-9th columns are the mean value across all positions + in the peak region. Refer to `narrowPeak` if you want to fix the + value issue in the 5th column. +5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both + the broad region and narrow peaks. The 5th column is the score for + showing grey levels on the UCSC browser as in `narrowPeak`. The 7th + is the start of the first narrow peak in the region, and the 8th + column is the end. The 9th column should be RGB color key, however, + we keep 0 here to use the default color, so change it if you + want. The 10th column tells how many blocks including the starting + 1bp and ending 1bp of broad regions. The 11th column shows the + length of each block and 12th for the start of each block. 13th: + fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can + be loaded directly to the UCSC genome browser. Refer to + `narrowPeak` if you want to fix the value issue in the 5th column. +6. `NAME_model.r` is an R script which you can use to produce a PDF + image of the model based on your data. Load it to R by: + `$ Rscript NAME_model.r` + Then a pdf file `NAME_model.pdf` will be generated in your current + directory. Note, R is required to draw this figure. +7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are + in bedGraph format which can be imported to the UCSC genome browser + or be converted into even smaller bigWig files. The + `NAME_treat_pielup.bdg` contains the pileup signals (normalized + according to `--scale-to` option) from ChIP/treatment sample. The + `NAME_control_lambda.bdg` contains local biases estimated for each + genomic location from the control sample, or from treatment sample + when the control sample is absent. The subcommand `bdgcmp` can be + used to compare these two files and make a bedGraph file of scores + such as p-value, q-value, log-likelihood, and log fold changes. +## Other useful links + * [Cistrome](http://cistrome.org/ap/) + * [bedTools](http://code.google.com/p/bedtools/) + * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/) +## Tips of fine-tuning peak calling +There are several subcommands within MACSv2 package to fine-tune or +customize your analysis: +1. `bdgcmp` can be used on `*_treat_pileup.bdg` and + `*_control_lambda.bdg` or bedGraph files from other resources to + calculate the score track. +2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file + generated from bdgcmp or bedGraph file from other resources to call + peaks with given cutoff, maximum-gap between nearby mergeable peaks + and a minimum length of peak. bdgbroadcall works similarly to + bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12 + format. +3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph + files which are scores between treatment 1 and control 1, treatment + 2 and control 2, treatment 1 and treatment 2, treatment 2 and + treatment 1. It will output consistent and unique sites according + to parameter settings for minimum length, the maximum gap and + cutoff. +4. You can combine subcommands to do a step-by-step peak calling. Read + detail at [MACS2 + wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands) + +%package -n python3-MACS2 +Summary: Model Based Analysis for ChIP-Seq data +Provides: python-MACS2 +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-MACS2 +`callpeak` | Main MACS2 Function to call peaks from alignment results. +`bdgpeakcall` | Call peaks from bedGraph output. +`bdgbroadcall` | Call broad peaks from bedGraph output. +`bdgcmp` | Comparing two signal tracks in bedGraph format. +`bdgopt` | Operate the score column of bedGraph file. +`cmbreps` | Combine BEDGraphs of scores from replicates. +`bdgdiff` | Differential peak detection based on paired four bedGraph files. +`filterdup` | Remove duplicate reads, then save in BED/BEDPE format. +`predictd` | Predict d or fragment size from alignment results. +`pileup` | Pileup aligned reads (single-end) or fragments (paired-end) +`randsample` | Randomly choose a number/percentage of total reads. +`refinepeak` | Take raw reads alignment, refine peak summits. +We only cover `callpeak` subcommand in this document. Please use +`macs2 COMMAND -h` to see the detail description for each option of +each subcommand. +### Call peaks +This is the main function in MACS2. It can be invoked by `macs2 +callpeak` . If you type this command with `-h`, you will see a full +description of command-line options. Here we only list the essentials. +#### Essential Options +##### `-t`/`--treatment FILENAME` +This is the only REQUIRED parameter for MACS. The file can be in any +supported format -- see detail in the `--format` option. If you have +more than one alignment file, you can specify them as `-t A B C`. MACS +will pool up all these files together. +##### `-c`/`--control` +The control, genomic input or mock IP data file. Please follow the +same direction as for `-t`/`--treatment`. +##### `-n`/`--name` +The name string of the experiment. MACS will use this string NAME to +create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`, +`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So +please avoid any confliction between these filenames and your existing +files. +##### `--outdir` +MACS2 will save all output files into the specified folder for this +option. A new folder will be created if necessary. +##### `-f`/`--format FORMAT` +Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`, +`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which +will allow MACS to decide the format automatically. `AUTO` is also +useful when you combine different formats of files. Note that MACS +can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to +implicitly specify the format for `BAMPE` and `BEDPE`. +Nowadays, the most common formats are `BED` or `BAM` (including +`BEDPE` and `BAMPE`). Our recommendation is to convert your data to +`BED` or `BAM` first. +Also, MACS2 can detect and read gzipped file. For example, `.bed.gz` +file can be directly used without being uncompressed with `--format +BED`. +Here are detailed explanation of the recommanded formats: +###### `BED` +The BED format can be found at [UCSC genome browser +website](http://genome.ucsc.edu/FAQ/FAQformat#format1). +The essential columns in BED format input are the 1st column +`chromosome name`, the 2nd `start position`, the 3rd `end position`, +and the 6th, `strand`. +Note that, for `BED` format, the 6th column of strand information is +required by MACS. And please pay attention that the coordinates in BED +format are zero-based and half-open. See more detail at +[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1). +###### `BAM`/`SAM` +If the format is `BAM`/`SAM`, please check the definition in +(http://samtools.sourceforge.net/samtools.shtml). If the `BAM` file is +generated for paired-end data, MACS will only keep the left mate(5' +end) tag. However, when format `BAMPE` is specified, MACS will use the +real fragments inferred from alignment results for reads pileup. +###### `BEDPE` or `BAMPE` +A special mode will be triggered while the format is specified as +`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED` +files as paired-end data. Instead of building a bimodal distribution +of plus and minus strand reads to predict fragment size, MACS2 will +use actual insert sizes of pairs of reads to build fragment pileup. +The `BAMPE` format is just a `BAM` format containing paired-end alignment +information, such as those from `BWA` or `BOWTIE`. +The `BEDPE` format is a simplified and more flexible `BED` format, +which only contains the first three columns defining the chromosome +name, left and right position of the fragment from Paired-end +sequencing. Please note, this is NOT the same format used by +`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a +standard `BED` format. You can use MACS2 subcommand `randsample` to +convert a `BAM` file containing paired-end information to a `BEDPE` +format file: +``` +macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed +``` +##### `-g`/`--gsize` +PLEASE assign this parameter to fit your needs! +It's the mappable genome size or effective genome size which is +defined as the genome size which can be sequenced. Because of the +repetitive features on the chromosomes, the actual mappable genome +size will be smaller than the original size, about 90% or 70% of the +genome size. The default *hs* -- 2.7e9 is recommended for human +genome. Here are all precompiled parameters for effective genome size: + * hs: 2.7e9 + * mm: 1.87e9 + * ce: 9e7 + * dm: 1.2e8 +Users may want to use k-mer tools to simulate mapping of Xbps long +reads to target genome, and to find the ideal effective genome +size. However, usually by taking away the simple repeats and Ns from +the total genome, one can get an approximate number of effective +genome size. A slight difference in the number won't cause a big +difference of peak calls, because this number is used to estimate a +genome-wide noise level which is usually the least significant one +compared with the *local biases* modeled by MACS. +##### `-s`/`--tsize` +The size of sequencing tags. If you don't specify it, MACS will try to +use the first 10 sequences from your input treatment file to determine +the tag size. Specifying it will override the automatically determined +tag size. +##### `-q`/`--qvalue` +The q-value (minimum FDR) cutoff to call significant regions. Default +is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are +calculated from p-values using the Benjamini-Hochberg procedure. +##### `-p`/`--pvalue` +The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead +of q-value. +##### `--min-length`, `--max-gap` +These two options can be used to fine-tune the peak calling behavior +by specifying the minimum length of a called peak and the maximum +allowed a gap between two nearby regions to be merged. In other words, +a called peak has to be longer than `min-length`, and if the distance +between two nearby peaks is smaller than `max-gap` then they will be +merged as one. If they are not set, MACS2 will set the DEFAULT value +for `min-length` as the predicted fragment size `d`, and the DEFAULT +value for `max-gap` as the detected read length. Note, if you set a +`min-length` value smaller than the fragment size, it may have NO +effect on the result. For broad peak calling with `--broad` option +set, the DEFAULT `max-gap` for merging nearby stronger peaks will be +the same as narrow peak calling, and 4 times of the `max-gap` will be +used to merge nearby weaker (broad) peaks. You can also use +`--cutoff-analysis` option with the default setting, and check the +column `avelpeak` under different cutoff values to decide a reasonable +`min-length` value. +##### `--nolambda` +With this flag on, MACS will use the background lambda as local +lambda. This means MACS will not consider the local bias at peak +candidate regions. +##### `--slocal`, `--llocal` +These two parameters control which two levels of regions will be +checked around the peak regions to calculate the maximum lambda as +local lambda. By default, MACS considers 1000bp for small local +region(`--slocal`), and 10000bps for large local region(`--llocal`) +which captures the bias from a long-range effect like an open +chromatin domain. You can tweak these according to your +project. Remember that if the region is set too small, a sharp spike +in the input data may kill a significant peak. +##### `--nomodel` +While on, MACS will bypass building the shifting model. +##### `--extsize` +While `--nomodel` is set, MACS uses this parameter to extend reads in +5'->3' direction to fix-sized fragments. For example, if the size of +the binding region for your transcription factor is 200 bp, and you +want to bypass the model building by MACS, this parameter can be set +as 200. This option is only valid when `--nomodel` is set or when MACS +fails to build model and `--fix-bimodal` is on. +##### `--shift` +Note, this is NOT the legacy `--shiftsize` option which is replaced by +`--extsize`! You can set an arbitrary shift in bp here. Please Use +discretion while setting it other than the default value (0). When +`--nomodel` is set, MACS will use this value to move cutting ends (5') +then apply `--extsize` from 5' to 3' direction to extend them to +fragments. When this value is negative, ends will be moved toward +3'->5' direction, otherwise 5'->3' direction. Recommended to keep it +as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together +with `--extsize` option for detecting enriched cutting loci such as +certain DNAseI-Seq datasets. Note, you can't set values other than 0 +if the format is BAMPE or BEDPE for paired-end data. The default is 0. +Here are some examples for combining `--shift` and `--extsize`: +1. To find enriched cutting sites such as some DNAse-Seq datasets. In +this case, all 5' ends of sequenced reads should be extended in both +directions to smooth the pileup signals. If the wanted smoothing +window is 200bps, then use `--nomodel --shift -100 --extsize 200`. +2. For certain nucleosome-seq data, we need to pile up the centers of +nucleosomes using a half-nucleosome size for wavelet analysis +(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about +147bps, this option can be used: `--nomodel --shift 37 --extsize 73`. +##### `--keep-dup` +It controls the MACS behavior towards duplicate tags at the exact same +location -- the same coordination and the same strand. The default +`auto` option makes MACS calculate the maximum tags at the exact same +location based on binomial distribution using 1e-5 as p-value cutoff; +and the `all` option keeps every tag. If an integer is given, at most +this number of tags will be kept at the same location. The default is +to keep one tag at the same location. Default: 1 +##### `--broad` +When this flag is on, MACS will try to composite broad regions in +BED12 ( a gene-model-like format ) by putting nearby highly enriched +regions into a broad region with loose cutoff. The broad region is +controlled by another cutoff through `--broad-cutoff`. Please note +that, the `max-gap` value for merging nearby weaker/broad peaks is 4 +times of `max-gap` for merging nearby stronger peaks. The later one +can be controlled by `--max-gap` option, and by default it is the +average fragment/insertion length in the PE data. DEFAULT: False +##### `--broad-cutoff` +Cutoff for the broad region. This option is not available unless +`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise, +it's a q-value cutoff. DEFAULT: 0.1 +##### `--scale-to <large|small>` +When set to `large`, linearly scale the smaller dataset to the same +depth as the larger dataset. By default or being set as `small`, the +larger dataset will be scaled towards the smaller dataset. Beware, to +scale up small data would cause more false positives. +##### `-B`/`--bdg` +If this flag is on, MACS will store the fragment pileup, control +lambda in bedGraph files. The bedGraph files will be stored in the +current directory named `NAME_treat_pileup.bdg` for treatment data, +`NAME_control_lambda.bdg` for local lambda values from control. +##### `--call-summits` +MACS will now reanalyze the shape of signal profile (p or q-score +depending on the cutoff setting) to deconvolve subpeaks within each +peak called from the general procedure. It's highly recommended to +detect adjacent binding events. While used, the output subpeaks of a +big peak region will have the same peak boundaries, and different +scores and peak summit positions. +##### `--buffer-size` +MACS uses a buffer size for incrementally increasing internal array +size to store reads alignment information for each chromosome or +contig. To increase the buffer size, MACS can run faster but will +waste more memory if certain chromosome/contig only has very few +reads. In most cases, the default value 100000 works fine. However, if +there are a large number of chromosomes/contigs in your alignment and +reads per chromosome/contigs are few, it's recommended to specify a +smaller buffer size in order to decrease memory usage (but it will +take longer time to read alignment files). Minimum memory requested +for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * +8 Bytes. DEFAULT: 100000 +#### Output files +1. `NAME_peaks.xls` is a tabular file which contains information about + called peaks. You can open it in excel and sort/filter using excel + functions. Information include: + - chromosome name + - start position of peak + - end position of peak + - length of peak region + - absolute peak summit position + - pileup height at peak summit + - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then + this value should be 10) + - fold enrichment for this peak summit against random Poisson + distribution with local lambda, + - -log10(qvalue) at peak summit + Coordinates in XLS is 1-based which is different from BED + format. When `--broad` is enabled for broad peak calling, the + pileup, p-value, q-value, and fold change in the XLS file will be + the mean value across the entire peak region, since peak summit + won't be called in broad peak calling mode. +2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the + peak locations together with peak summit, p-value, and q-value. You + can load it to the UCSC genome browser. Definition of some specific + columns are: + - 5th: integer score for display. It's calculated as + `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on + whether `-p` (pvalue) or `-q` (qvalue) is used as score + cutoff. Please note that currently this value might be out of the + [0-1000] range defined in [UCSC ENCODE narrowPeak + format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You + can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by + using the following 1-liner awk: `awk -v OFS="\t" + '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak` + - 7th: fold-change at peak summit + - 8th: -log10pvalue at peak summit + - 9th: -log10qvalue at peak summit + - 10th: relative summit position to peak start + The file can be loaded directly to the UCSC genome browser. Remove + the beginning track line if you want to analyze it by other tools. +3. `NAME_summits.bed` is in BED format, which contains the peak + summits locations for every peak. The 5th column in this file is + the same as what is in the `narrowPeak` file. If you want to find + the motifs at the binding sites, this file is recommended. The file + can be loaded directly to the UCSC genome browser. Remove the + beginning track line if you want to analyze it by other tools. +4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to + `narrowPeak` file, except for missing the 10th column for + annotating peak summits. This file and the `gappedPeak` file will + only be available when `--broad` is enabled. Since in the broad + peak calling mode, the peak summit won't be called, the values in + the 5th, and 7-9th columns are the mean value across all positions + in the peak region. Refer to `narrowPeak` if you want to fix the + value issue in the 5th column. +5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both + the broad region and narrow peaks. The 5th column is the score for + showing grey levels on the UCSC browser as in `narrowPeak`. The 7th + is the start of the first narrow peak in the region, and the 8th + column is the end. The 9th column should be RGB color key, however, + we keep 0 here to use the default color, so change it if you + want. The 10th column tells how many blocks including the starting + 1bp and ending 1bp of broad regions. The 11th column shows the + length of each block and 12th for the start of each block. 13th: + fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can + be loaded directly to the UCSC genome browser. Refer to + `narrowPeak` if you want to fix the value issue in the 5th column. +6. `NAME_model.r` is an R script which you can use to produce a PDF + image of the model based on your data. Load it to R by: + `$ Rscript NAME_model.r` + Then a pdf file `NAME_model.pdf` will be generated in your current + directory. Note, R is required to draw this figure. +7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are + in bedGraph format which can be imported to the UCSC genome browser + or be converted into even smaller bigWig files. The + `NAME_treat_pielup.bdg` contains the pileup signals (normalized + according to `--scale-to` option) from ChIP/treatment sample. The + `NAME_control_lambda.bdg` contains local biases estimated for each + genomic location from the control sample, or from treatment sample + when the control sample is absent. The subcommand `bdgcmp` can be + used to compare these two files and make a bedGraph file of scores + such as p-value, q-value, log-likelihood, and log fold changes. +## Other useful links + * [Cistrome](http://cistrome.org/ap/) + * [bedTools](http://code.google.com/p/bedtools/) + * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/) +## Tips of fine-tuning peak calling +There are several subcommands within MACSv2 package to fine-tune or +customize your analysis: +1. `bdgcmp` can be used on `*_treat_pileup.bdg` and + `*_control_lambda.bdg` or bedGraph files from other resources to + calculate the score track. +2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file + generated from bdgcmp or bedGraph file from other resources to call + peaks with given cutoff, maximum-gap between nearby mergeable peaks + and a minimum length of peak. bdgbroadcall works similarly to + bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12 + format. +3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph + files which are scores between treatment 1 and control 1, treatment + 2 and control 2, treatment 1 and treatment 2, treatment 2 and + treatment 1. It will output consistent and unique sites according + to parameter settings for minimum length, the maximum gap and + cutoff. +4. You can combine subcommands to do a step-by-step peak calling. Read + detail at [MACS2 + wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands) + +%package help +Summary: Development documents and examples for MACS2 +Provides: python3-MACS2-doc +%description help +`callpeak` | Main MACS2 Function to call peaks from alignment results. +`bdgpeakcall` | Call peaks from bedGraph output. +`bdgbroadcall` | Call broad peaks from bedGraph output. +`bdgcmp` | Comparing two signal tracks in bedGraph format. +`bdgopt` | Operate the score column of bedGraph file. +`cmbreps` | Combine BEDGraphs of scores from replicates. +`bdgdiff` | Differential peak detection based on paired four bedGraph files. +`filterdup` | Remove duplicate reads, then save in BED/BEDPE format. +`predictd` | Predict d or fragment size from alignment results. +`pileup` | Pileup aligned reads (single-end) or fragments (paired-end) +`randsample` | Randomly choose a number/percentage of total reads. +`refinepeak` | Take raw reads alignment, refine peak summits. +We only cover `callpeak` subcommand in this document. Please use +`macs2 COMMAND -h` to see the detail description for each option of +each subcommand. +### Call peaks +This is the main function in MACS2. It can be invoked by `macs2 +callpeak` . If you type this command with `-h`, you will see a full +description of command-line options. Here we only list the essentials. +#### Essential Options +##### `-t`/`--treatment FILENAME` +This is the only REQUIRED parameter for MACS. The file can be in any +supported format -- see detail in the `--format` option. If you have +more than one alignment file, you can specify them as `-t A B C`. MACS +will pool up all these files together. +##### `-c`/`--control` +The control, genomic input or mock IP data file. Please follow the +same direction as for `-t`/`--treatment`. +##### `-n`/`--name` +The name string of the experiment. MACS will use this string NAME to +create output files like `NAME_peaks.xls`, `NAME_negative_peaks.xls`, +`NAME_peaks.bed` , `NAME_summits.bed`, `NAME_model.r` and so on. So +please avoid any confliction between these filenames and your existing +files. +##### `--outdir` +MACS2 will save all output files into the specified folder for this +option. A new folder will be created if necessary. +##### `-f`/`--format FORMAT` +Format of tag file can be `ELAND`, `BED`, `ELANDMULTI`, `ELANDEXPORT`, +`SAM`, `BAM`, `BOWTIE`, `BAMPE`, or `BEDPE`. Default is `AUTO` which +will allow MACS to decide the format automatically. `AUTO` is also +useful when you combine different formats of files. Note that MACS +can't detect `BAMPE` or `BEDPE` format with `AUTO`, and you have to +implicitly specify the format for `BAMPE` and `BEDPE`. +Nowadays, the most common formats are `BED` or `BAM` (including +`BEDPE` and `BAMPE`). Our recommendation is to convert your data to +`BED` or `BAM` first. +Also, MACS2 can detect and read gzipped file. For example, `.bed.gz` +file can be directly used without being uncompressed with `--format +BED`. +Here are detailed explanation of the recommanded formats: +###### `BED` +The BED format can be found at [UCSC genome browser +website](http://genome.ucsc.edu/FAQ/FAQformat#format1). +The essential columns in BED format input are the 1st column +`chromosome name`, the 2nd `start position`, the 3rd `end position`, +and the 6th, `strand`. +Note that, for `BED` format, the 6th column of strand information is +required by MACS. And please pay attention that the coordinates in BED +format are zero-based and half-open. See more detail at +[UCSC site](http://genome.ucsc.edu/FAQ/FAQtracks#tracks1). +###### `BAM`/`SAM` +If the format is `BAM`/`SAM`, please check the definition in +(http://samtools.sourceforge.net/samtools.shtml). If the `BAM` file is +generated for paired-end data, MACS will only keep the left mate(5' +end) tag. However, when format `BAMPE` is specified, MACS will use the +real fragments inferred from alignment results for reads pileup. +###### `BEDPE` or `BAMPE` +A special mode will be triggered while the format is specified as +`BAMPE` or `BEDPE`. In this way, MACS2 will process the `BAM` or `BED` +files as paired-end data. Instead of building a bimodal distribution +of plus and minus strand reads to predict fragment size, MACS2 will +use actual insert sizes of pairs of reads to build fragment pileup. +The `BAMPE` format is just a `BAM` format containing paired-end alignment +information, such as those from `BWA` or `BOWTIE`. +The `BEDPE` format is a simplified and more flexible `BED` format, +which only contains the first three columns defining the chromosome +name, left and right position of the fragment from Paired-end +sequencing. Please note, this is NOT the same format used by +`BEDTOOLS`, and the `BEDTOOLS` version of `BEDPE` is actually not in a +standard `BED` format. You can use MACS2 subcommand `randsample` to +convert a `BAM` file containing paired-end information to a `BEDPE` +format file: +``` +macs2 randsample -i the_BAMPE_file.bam -f BAMPE -p 100 -o the_BEDPE_file.bed +``` +##### `-g`/`--gsize` +PLEASE assign this parameter to fit your needs! +It's the mappable genome size or effective genome size which is +defined as the genome size which can be sequenced. Because of the +repetitive features on the chromosomes, the actual mappable genome +size will be smaller than the original size, about 90% or 70% of the +genome size. The default *hs* -- 2.7e9 is recommended for human +genome. Here are all precompiled parameters for effective genome size: + * hs: 2.7e9 + * mm: 1.87e9 + * ce: 9e7 + * dm: 1.2e8 +Users may want to use k-mer tools to simulate mapping of Xbps long +reads to target genome, and to find the ideal effective genome +size. However, usually by taking away the simple repeats and Ns from +the total genome, one can get an approximate number of effective +genome size. A slight difference in the number won't cause a big +difference of peak calls, because this number is used to estimate a +genome-wide noise level which is usually the least significant one +compared with the *local biases* modeled by MACS. +##### `-s`/`--tsize` +The size of sequencing tags. If you don't specify it, MACS will try to +use the first 10 sequences from your input treatment file to determine +the tag size. Specifying it will override the automatically determined +tag size. +##### `-q`/`--qvalue` +The q-value (minimum FDR) cutoff to call significant regions. Default +is 0.05. For broad marks, you can try 0.05 as the cutoff. Q-values are +calculated from p-values using the Benjamini-Hochberg procedure. +##### `-p`/`--pvalue` +The p-value cutoff. If `-p` is specified, MACS2 will use p-value instead +of q-value. +##### `--min-length`, `--max-gap` +These two options can be used to fine-tune the peak calling behavior +by specifying the minimum length of a called peak and the maximum +allowed a gap between two nearby regions to be merged. In other words, +a called peak has to be longer than `min-length`, and if the distance +between two nearby peaks is smaller than `max-gap` then they will be +merged as one. If they are not set, MACS2 will set the DEFAULT value +for `min-length` as the predicted fragment size `d`, and the DEFAULT +value for `max-gap` as the detected read length. Note, if you set a +`min-length` value smaller than the fragment size, it may have NO +effect on the result. For broad peak calling with `--broad` option +set, the DEFAULT `max-gap` for merging nearby stronger peaks will be +the same as narrow peak calling, and 4 times of the `max-gap` will be +used to merge nearby weaker (broad) peaks. You can also use +`--cutoff-analysis` option with the default setting, and check the +column `avelpeak` under different cutoff values to decide a reasonable +`min-length` value. +##### `--nolambda` +With this flag on, MACS will use the background lambda as local +lambda. This means MACS will not consider the local bias at peak +candidate regions. +##### `--slocal`, `--llocal` +These two parameters control which two levels of regions will be +checked around the peak regions to calculate the maximum lambda as +local lambda. By default, MACS considers 1000bp for small local +region(`--slocal`), and 10000bps for large local region(`--llocal`) +which captures the bias from a long-range effect like an open +chromatin domain. You can tweak these according to your +project. Remember that if the region is set too small, a sharp spike +in the input data may kill a significant peak. +##### `--nomodel` +While on, MACS will bypass building the shifting model. +##### `--extsize` +While `--nomodel` is set, MACS uses this parameter to extend reads in +5'->3' direction to fix-sized fragments. For example, if the size of +the binding region for your transcription factor is 200 bp, and you +want to bypass the model building by MACS, this parameter can be set +as 200. This option is only valid when `--nomodel` is set or when MACS +fails to build model and `--fix-bimodal` is on. +##### `--shift` +Note, this is NOT the legacy `--shiftsize` option which is replaced by +`--extsize`! You can set an arbitrary shift in bp here. Please Use +discretion while setting it other than the default value (0). When +`--nomodel` is set, MACS will use this value to move cutting ends (5') +then apply `--extsize` from 5' to 3' direction to extend them to +fragments. When this value is negative, ends will be moved toward +3'->5' direction, otherwise 5'->3' direction. Recommended to keep it +as default 0 for ChIP-Seq datasets, or -1 * half of *EXTSIZE* together +with `--extsize` option for detecting enriched cutting loci such as +certain DNAseI-Seq datasets. Note, you can't set values other than 0 +if the format is BAMPE or BEDPE for paired-end data. The default is 0. +Here are some examples for combining `--shift` and `--extsize`: +1. To find enriched cutting sites such as some DNAse-Seq datasets. In +this case, all 5' ends of sequenced reads should be extended in both +directions to smooth the pileup signals. If the wanted smoothing +window is 200bps, then use `--nomodel --shift -100 --extsize 200`. +2. For certain nucleosome-seq data, we need to pile up the centers of +nucleosomes using a half-nucleosome size for wavelet analysis +(e.g. NPS algorithm). Since the DNA wrapped on nucleosome is about +147bps, this option can be used: `--nomodel --shift 37 --extsize 73`. +##### `--keep-dup` +It controls the MACS behavior towards duplicate tags at the exact same +location -- the same coordination and the same strand. The default +`auto` option makes MACS calculate the maximum tags at the exact same +location based on binomial distribution using 1e-5 as p-value cutoff; +and the `all` option keeps every tag. If an integer is given, at most +this number of tags will be kept at the same location. The default is +to keep one tag at the same location. Default: 1 +##### `--broad` +When this flag is on, MACS will try to composite broad regions in +BED12 ( a gene-model-like format ) by putting nearby highly enriched +regions into a broad region with loose cutoff. The broad region is +controlled by another cutoff through `--broad-cutoff`. Please note +that, the `max-gap` value for merging nearby weaker/broad peaks is 4 +times of `max-gap` for merging nearby stronger peaks. The later one +can be controlled by `--max-gap` option, and by default it is the +average fragment/insertion length in the PE data. DEFAULT: False +##### `--broad-cutoff` +Cutoff for the broad region. This option is not available unless +`--broad` is set. If `-p` is set, this is a p-value cutoff, otherwise, +it's a q-value cutoff. DEFAULT: 0.1 +##### `--scale-to <large|small>` +When set to `large`, linearly scale the smaller dataset to the same +depth as the larger dataset. By default or being set as `small`, the +larger dataset will be scaled towards the smaller dataset. Beware, to +scale up small data would cause more false positives. +##### `-B`/`--bdg` +If this flag is on, MACS will store the fragment pileup, control +lambda in bedGraph files. The bedGraph files will be stored in the +current directory named `NAME_treat_pileup.bdg` for treatment data, +`NAME_control_lambda.bdg` for local lambda values from control. +##### `--call-summits` +MACS will now reanalyze the shape of signal profile (p or q-score +depending on the cutoff setting) to deconvolve subpeaks within each +peak called from the general procedure. It's highly recommended to +detect adjacent binding events. While used, the output subpeaks of a +big peak region will have the same peak boundaries, and different +scores and peak summit positions. +##### `--buffer-size` +MACS uses a buffer size for incrementally increasing internal array +size to store reads alignment information for each chromosome or +contig. To increase the buffer size, MACS can run faster but will +waste more memory if certain chromosome/contig only has very few +reads. In most cases, the default value 100000 works fine. However, if +there are a large number of chromosomes/contigs in your alignment and +reads per chromosome/contigs are few, it's recommended to specify a +smaller buffer size in order to decrease memory usage (but it will +take longer time to read alignment files). Minimum memory requested +for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * +8 Bytes. DEFAULT: 100000 +#### Output files +1. `NAME_peaks.xls` is a tabular file which contains information about + called peaks. You can open it in excel and sort/filter using excel + functions. Information include: + - chromosome name + - start position of peak + - end position of peak + - length of peak region + - absolute peak summit position + - pileup height at peak summit + - -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then + this value should be 10) + - fold enrichment for this peak summit against random Poisson + distribution with local lambda, + - -log10(qvalue) at peak summit + Coordinates in XLS is 1-based which is different from BED + format. When `--broad` is enabled for broad peak calling, the + pileup, p-value, q-value, and fold change in the XLS file will be + the mean value across the entire peak region, since peak summit + won't be called in broad peak calling mode. +2. `NAME_peaks.narrowPeak` is BED6+4 format file which contains the + peak locations together with peak summit, p-value, and q-value. You + can load it to the UCSC genome browser. Definition of some specific + columns are: + - 5th: integer score for display. It's calculated as + `int(-10*log10pvalue)` or `int(-10*log10qvalue)` depending on + whether `-p` (pvalue) or `-q` (qvalue) is used as score + cutoff. Please note that currently this value might be out of the + [0-1000] range defined in [UCSC ENCODE narrowPeak + format](https://genome.ucsc.edu/FAQ/FAQformat.html#format12). You + can let the value saturated at 1000 (i.e. p/q-value = 10^-100) by + using the following 1-liner awk: `awk -v OFS="\t" + '{$5=$5>1000?1000:$5} {print}' NAME_peaks.narrowPeak` + - 7th: fold-change at peak summit + - 8th: -log10pvalue at peak summit + - 9th: -log10qvalue at peak summit + - 10th: relative summit position to peak start + The file can be loaded directly to the UCSC genome browser. Remove + the beginning track line if you want to analyze it by other tools. +3. `NAME_summits.bed` is in BED format, which contains the peak + summits locations for every peak. The 5th column in this file is + the same as what is in the `narrowPeak` file. If you want to find + the motifs at the binding sites, this file is recommended. The file + can be loaded directly to the UCSC genome browser. Remove the + beginning track line if you want to analyze it by other tools. +4. `NAME_peaks.broadPeak` is in BED6+3 format which is similar to + `narrowPeak` file, except for missing the 10th column for + annotating peak summits. This file and the `gappedPeak` file will + only be available when `--broad` is enabled. Since in the broad + peak calling mode, the peak summit won't be called, the values in + the 5th, and 7-9th columns are the mean value across all positions + in the peak region. Refer to `narrowPeak` if you want to fix the + value issue in the 5th column. +5. `NAME_peaks.gappedPeak` is in BED12+3 format which contains both + the broad region and narrow peaks. The 5th column is the score for + showing grey levels on the UCSC browser as in `narrowPeak`. The 7th + is the start of the first narrow peak in the region, and the 8th + column is the end. The 9th column should be RGB color key, however, + we keep 0 here to use the default color, so change it if you + want. The 10th column tells how many blocks including the starting + 1bp and ending 1bp of broad regions. The 11th column shows the + length of each block and 12th for the start of each block. 13th: + fold-change, 14th: *-log10pvalue*, 15th: *-log10qvalue*. The file can + be loaded directly to the UCSC genome browser. Refer to + `narrowPeak` if you want to fix the value issue in the 5th column. +6. `NAME_model.r` is an R script which you can use to produce a PDF + image of the model based on your data. Load it to R by: + `$ Rscript NAME_model.r` + Then a pdf file `NAME_model.pdf` will be generated in your current + directory. Note, R is required to draw this figure. +7. The `NAME_treat_pileup.bdg` and `NAME_control_lambda.bdg` files are + in bedGraph format which can be imported to the UCSC genome browser + or be converted into even smaller bigWig files. The + `NAME_treat_pielup.bdg` contains the pileup signals (normalized + according to `--scale-to` option) from ChIP/treatment sample. The + `NAME_control_lambda.bdg` contains local biases estimated for each + genomic location from the control sample, or from treatment sample + when the control sample is absent. The subcommand `bdgcmp` can be + used to compare these two files and make a bedGraph file of scores + such as p-value, q-value, log-likelihood, and log fold changes. +## Other useful links + * [Cistrome](http://cistrome.org/ap/) + * [bedTools](http://code.google.com/p/bedtools/) + * [UCSC toolkits](http://hgdownload.cse.ucsc.edu/admin/exe/) +## Tips of fine-tuning peak calling +There are several subcommands within MACSv2 package to fine-tune or +customize your analysis: +1. `bdgcmp` can be used on `*_treat_pileup.bdg` and + `*_control_lambda.bdg` or bedGraph files from other resources to + calculate the score track. +2. `bdgpeakcall` can be used on `*_treat_pvalue.bdg` or the file + generated from bdgcmp or bedGraph file from other resources to call + peaks with given cutoff, maximum-gap between nearby mergeable peaks + and a minimum length of peak. bdgbroadcall works similarly to + bdgpeakcall, however, it will output `_broad_peaks.bed` in BED12 + format. +3. Differential calling tool -- `bdgdiff`, can be used on 4 bedGraph + files which are scores between treatment 1 and control 1, treatment + 2 and control 2, treatment 1 and treatment 2, treatment 2 and + treatment 1. It will output consistent and unique sites according + to parameter settings for minimum length, the maximum gap and + cutoff. +4. You can combine subcommands to do a step-by-step peak calling. Read + detail at [MACS2 + wikipage](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands) + +%prep +%autosetup -n MACS2-2.2.7.1 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-MACS2 -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 2.2.7.1-1 +- Package Spec generated |