Macs2 - Revision history

Rf at 22:54, 7 August 2017

2017-08-07T22:54:07Z

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2017-07-12T09:55:00Z

Rf at 12:27, 29 June 2017

2017-06-29T12:27:06Z

Rf at 16:15, 5 June 2017

2017-06-05T16:15:37Z

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2017-06-05T16:12:23Z

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Rf at 12:54, 5 June 2017

2017-06-05T12:54:58Z

Rf at 10:53, 5 June 2017

2017-06-05T10:53:58Z

Rf: Created page with "= Introduction = One of the main programs used for peak-calling on ChIP-Seq alignments. = Usage = == Help file == Here is the programs help file obtained with the command..."

2017-05-22T16:49:03Z

Created page with "= Introduction = One of the main programs used for peak-calling on ChIP-Seq alignments. = Usage = == Help file == Here is the programs help file obtained with the command..."

New page

= Introduction =

One of the main programs used for peak-calling on ChIP-Seq alignments.

= Usage =

== Help file ==
Here is the programs help file obtained with the command

macs2 -h

macs2 -- Model-based Analysis for ChIP-Sequencing

positional arguments:
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
callpeak Main MACS2 Function: Call peaks from alignment
results.
bdgpeakcall Call peaks from bedGraph output. Note: All regions on
the same chromosome in the bedGraph file should be
continuous so only bedGraph files from MACS2 are
accpetable.
bdgbroadcall Call broad peaks from bedGraph output. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
bdgcmp Deduct noise by comparing two signal tracks in
bedGraph. Note: All regions on the same chromosome in
the bedGraph file should be continuous so only
bedGraph files from MACS2 are accpetable.
bdgopt Operations on score column of bedGraph file. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
cmbreps Combine BEDGraphs of scores from replicates. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
bdgdiff Differential peak detection based on paired four
bedgraph files. Note: All regions on the same
chromosome in the bedGraph file should be continuous
so only bedGraph files from MACS2 are accpetable.
filterdup Remove duplicate reads at the same position, then
convert acceptable format to BED format.
predictd Predict d or fragment size from alignment results.
*Will NOT filter duplicates*
pileup Pileup aligned reads with a given extension size
(fragment size or d in MACS language). Note there will
be no step for duplicate reads filtering or sequencing
depth scaling, so you may need to do certain pre/post-
processing.
randsample Randomly sample number/percentage of total reads.
refinepeak (Experimental) Take raw reads alignment, refine peak
summits and give scores measuring balance of
waston/crick tags. Inspired by SPP.

optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit

← Older revision		Revision as of 22:54, 7 August 2017
Line 191:		Line 191:
	-h, --help show this help message and exit		-h, --help show this help message and exit
	--version show program's version number and exit		--version show program's version number and exit
		+
		+	= Links =
		+	* The [https://github.com/taoliu/MACS/wiki wiki] gives extra information beyond the main help page.
		+	* [https://github.com/taoliu/MACS/wiki/Build-Signal-Track building the signal track], this is mainly about bdgcmp.

@@ Line 77: / Line 77: @@
 === unsuccessful output ===
-For comparison purposes, it may be useful to have this, a fualty run because '''-f BAMPE''' was not specified.
+For comparison purposes, it may be useful to have this, a faulty run because '''-f BAMPE''' was not specified.
   INFO  @ Fri, 02 Jun 2017 18:29:17:

← Older revision		Revision as of 12:27, 29 June 2017
Line 6:		Line 6:

	Here are some example usages. The module must be loaded via <code>module load macs2</code>.		Here are some example usages. The module must be loaded via <code>module load macs2</code>.
		+
		+	== Differential peak calling ==
		+
		+	Macs does claim to be able to this, though there are specialized packages out there (Thor). [https://github.com/taoliu/MACS/wiki/Call-differential-binding-events Here] is a link to Macs2's documentation on the subject.

	== base minimum options ==		== base minimum options ==

@@ Line 73: / Line 73: @@
 === unsuccessful output ===
-For comparison purposes, it may be useful to have this:
+For comparison purposes, it may be useful to have this, a fualty run because '''-f BAMPE''' was not specified.
   INFO  @ Fri, 02 Jun 2017 18:29:17:
   # Command line: callpeak -t USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.01
@@ Line 172: / Line 134: @@
   the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.
   WARNING @ Fri, 02 Jun 2017 18:31:02: Process for pairing-model is terminated!
 == Help file ==

@@ Line 15: / Line 15: @@
 * '''-g''', this is the genome size, which you can calculate by coutning all the bases int he reference FASTA
 * '''-q''', is a quality values ... have seen 0.1 to 0.01 being used.
-* ''-f BAMPE''', allows to specify we are dealing with paired-end reads.
+* '''-f BAMPE''', allows to specify we are dealing with paired-end reads.
 === output from this command ===
   INFO  @ Fri, 02 Jun 2017 18:27:43:

@@ Line 9: / Line 9: @@
 == base minimum options ==
- macs2 callpeak -t ULS1IP_S7_L001/ULS1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.010
+  macs2 callpeak -t USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -f BAMPE -g 11.1e6 -q 0.01
 <ins>Explanation</ins>:
 * '''-g''', this is the genome size, which you can calculate by coutning all the bases int he reference FASTA
 * '''-q''', is a quality values ... have seen 0.1 to 0.01 being used.
-* missing, '''-f BAMPE''' as actually we were dealign with paired0-end reads
+* ''-f BAMPE''', allows to specify we are dealing with paired-end reads.
 === output from this command ===

← Older revision		Revision as of 10:53, 5 June 2017
Line 4:		Line 4:

	= Usage =		= Usage =
		+
		+	Here are some example usages. The module must be loaded via <code>module load macs2</code>.
		+
		+	== base minimum options ==
		+
		+	macs2 callpeak -t ULS1IP_S7_L001/ULS1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.010
		+
		+
		+	<ins>Explanation</ins>:
		+	* '''-g''', this is the genome size, which you can calculate by coutning all the bases int he reference FASTA
		+	* '''-q''', is a quality values ... have seen 0.1 to 0.01 being used.
		+	* missing, the bampe mode.
		+
		+	=== output from this command ===
		+
		+	INFO @ Fri, 02 Jun 2017 18:27:43:
		+	# Command line: callpeak -t ULS1IP_S7_L001/ULS1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.01
		+	# ARGUMENTS LIST:
		+	# name = NA
		+	# format = AUTO
		+	# ChIP-seq file = ['ULS1IP_S7_L001/ULS1IP_S7_L001_srtd.bam']
		+	# control file = ['ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam']
		+	# effective genome size = 1.11e+07
		+	# band width = 300
		+	# model fold = [5, 50]
		+	# qvalue cutoff = 1.00e-02
		+	# Larger dataset will be scaled towards smaller dataset.
		+	# Range for calculating regional lambda is: 1000 bps and 10000 bps
		+	# Broad region calling is off
		+	# Paired-End mode is off
		+
		+	INFO @ Fri, 02 Jun 2017 18:27:43: #1 read tag files...
		+	INFO @ Fri, 02 Jun 2017 18:27:43: #1 read treatment tags...
		+	Traceback (most recent call last):
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/bin/macs2", line 617, in <module>
		+	main()
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/bin/macs2", line 57, in main
		+	run( args )
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 73, in run
		+	else: (treat, control) = load_tag_files_options (options)
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 395, in load_tag_files_options
		+	tp = options.parser(options.tfile[0], buffer_size=options.buffer_size)
		+	File "MACS2/IO/Parser.pyx", line 58, in MACS2.IO.Parser.guess_parser (MACS2/IO/Parser.c:2786)
		+	File "MACS2/IO/Parser.pyx", line 81, in MACS2.IO.Parser.guess_parser (MACS2/IO/Parser.c:2413)
		+	File "MACS2/IO/Parser.pyx", line 774, in MACS2.IO.Parser.BAMParser.__init__ (MACS2/IO/Parser.c:11146)
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/lib/python2.7/gzip.py", line 34, in open
		+	return GzipFile(filename, mode, compresslevel)
		+	File "/usr/local/Modules/modulefiles/tools/python/2.7.6/lib/python2.7/gzip.py", line 94, in __init__
		+	fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
		+	IOError: [Errno 2] No such file or directory: 'ULS1IP_S7_L001/ULS1IP_S7_L001_srtd.bam'
		+	[ramon@marvin SeqAH_proj0]$ ls -l U
		+	ULS1INP_S6_L001/ ULS1INP_S6_L002/ ULS1INP_S6_L003/ ULS1INP_S6_L004/ USL1IP_S7_L001/ USL1IP_S7_L002/ USL1IP_S7_L003/ USL1IP_S7_L004/
		+	[ramon@marvin SeqAH_proj0]$ macs2 callpeak -t USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.01
		+	INFO @ Fri, 02 Jun 2017 18:29:17:
		+	# Command line: callpeak -t USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam -c ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam -g 11.1e6 -q0.01
		+	# ARGUMENTS LIST:
		+	# name = NA
		+	# format = AUTO
		+	# ChIP-seq file = ['USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam']
		+	# control file = ['ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam']
		+	# effective genome size = 1.11e+07
		+	# band width = 300
		+	# model fold = [5, 50]
		+	# qvalue cutoff = 1.00e-02
		+	# Larger dataset will be scaled towards smaller dataset.
		+	# Range for calculating regional lambda is: 1000 bps and 10000 bps
		+	# Broad region calling is off
		+	# Paired-End mode is off
		+
		+	INFO @ Fri, 02 Jun 2017 18:29:17: #1 read tag files...
		+	INFO @ Fri, 02 Jun 2017 18:29:17: #1 read treatment tags...
		+	INFO @ Fri, 02 Jun 2017 18:29:17: Detected format is: BAM
		+	INFO @ Fri, 02 Jun 2017 18:29:17: * Input file is gzipped.
		+	INFO @ Fri, 02 Jun 2017 18:29:23: 1000000
		+	INFO @ Fri, 02 Jun 2017 18:29:29: 2000000
		+	INFO @ Fri, 02 Jun 2017 18:29:35: 3000000
		+	INFO @ Fri, 02 Jun 2017 18:29:41: 4000000
		+	INFO @ Fri, 02 Jun 2017 18:29:42: #1.2 read input tags...
		+	INFO @ Fri, 02 Jun 2017 18:29:42: Detected format is: BAM
		+	INFO @ Fri, 02 Jun 2017 18:29:42: * Input file is gzipped.
		+	INFO @ Fri, 02 Jun 2017 18:29:48: 1000000
		+	INFO @ Fri, 02 Jun 2017 18:29:55: 2000000
		+	INFO @ Fri, 02 Jun 2017 18:30:01: 3000000
		+	INFO @ Fri, 02 Jun 2017 18:30:07: 4000000
		+	INFO @ Fri, 02 Jun 2017 18:30:13: 5000000
		+	INFO @ Fri, 02 Jun 2017 18:30:19: 6000000
		+	INFO @ Fri, 02 Jun 2017 18:30:25: 7000000
		+	INFO @ Fri, 02 Jun 2017 18:30:32: 8000000
		+	INFO @ Fri, 02 Jun 2017 18:30:38: 9000000
		+	INFO @ Fri, 02 Jun 2017 18:30:44: 10000000
		+	INFO @ Fri, 02 Jun 2017 18:30:50: 11000000
		+	INFO @ Fri, 02 Jun 2017 18:30:56: 12000000
		+	INFO @ Fri, 02 Jun 2017 18:31:02: 13000000
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 tag size is determined as 59 bps
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 tag size = 59
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 total tags in treatment: 2013032
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 user defined the maximum tags...
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 tags after filtering in treatment: 1208158
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 Redundant rate of treatment: 0.40
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 total tags in control: 6333991
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 user defined the maximum tags...
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 tags after filtering in control: 4408839
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 Redundant rate of control: 0.30
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #1 finished!
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #2 Build Peak Model...
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #2 looking for paired plus/minus strand peaks...
		+	INFO @ Fri, 02 Jun 2017 18:31:02: #2 number of paired peaks: 61
		+	WARNING @ Fri, 02 Jun 2017 18:31:02: Too few paired peaks (61) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build
		+	the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.
		+	WARNING @ Fri, 02 Jun 2017 18:31:02: Process for pairing-model is terminated!
		+

	== Help file ==		== Help file ==