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  • which one is better for paired-ends peak calling? MACS2 OR MACS14?

    Hello,

    I'am working on paired-ends chip-seq analysis.

    Which one is better for peak calling? macs2 OR macs14?

    I ran both of them, macs2 has less peaks than macs14.

    Thanks in advance for any help!

    With Best!


    Yue Li

  • #2
    Hi, @Yue Li

    Did you find an answer for your question?

    I am analysing ChIP-Seq data and I used MACS2. How may peaks did you get? I had to use q=0.005 (minimum FDR (q-value) cutoff for peak detection) to reduce number of called peaks. And I have got ~30k. I worry it is too many.
    I will appreciate your feedback.

    Comment


    • #3
      Hello, @KB

      Flollwing is my command, qvalue cutoff = 5.00e-02. I got peaks around 400.




      If using paired end reads use “--format BAMPE” to let MACS2 pileup the whole
      fragments in general. If you want to focus on looking for where the 'cutting sites' are, then
      “--nomodel --shift -100 --extsize 200” should work.

      Since the DNA wrapped on a nucleosome is about 147bp, for single nucleosome detection

      use “ --nomodel --shift -37 --extsize 73

      INFO @ Thu, 21 Mar 2019 12:30:48: #1 fragment size = 2729.7


      Please free to contract me if you have any questions.

      Best,

      Yue

      administrator@ACB-HuangLab-Ubuntu:~/MACS2-2.1.2$ macs2 callpeak -t myc1_marked_duplicates.bam -c control_marked_duplicates.bam -f BAMPE -g hs -n myc1 -B --nomodel --shift -100 --extsize 200 --slocal 3000

      /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning: /home/administrator/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).

      warnings.warn(msg, UserWarning)

      INFO @ Fri, 22 Mar 2019 12:34:52:

      # Command line: callpeak -t myc1_marked_duplicates.bam -c control_marked_duplicates.bam -f BAMPE -g hs -n myc1 -B --nomodel --shift -100 --extsize 200 --slocal 3000

      # ARGUMENTS LIST:

      # name = myc1

      # format = BAMPE

      # ChIP-seq file = ['myc1_marked_duplicates.bam']

      # control file = ['control_marked_duplicates.bam']

      # effective genome size = 2.70e+09

      # band width = 300

      # model fold = [5, 50]

      # qvalue cutoff = 5.00e-02

      # The maximum gap between significant sites is assigned as the read length/tag size.

      # The minimum length of peaks is assigned as the predicted fragment length "d".

      # Larger dataset will be scaled towards smaller dataset.

      # Range for calculating regional lambda is: 3000 bps and 10000 bps

      # Broad region calling is off

      # Paired-End mode is on



      INFO @ Fri, 22 Mar 2019 12:34:52: #1 read fragment files...

      INFO @ Fri, 22 Mar 2019 12:34:52: #1 read treatment fragments...

      INFO @ Fri, 22 Mar 2019 12:34:58: 1000000

      INFO @ Fri, 22 Mar 2019 12:35:10: 2000000

      INFO @ Fri, 22 Mar 2019 12:35:17: 3000000

      INFO @ Fri, 22 Mar 2019 12:35:24: 4000000

      INFO @ Fri, 22 Mar 2019 12:35:31: 5000000

      INFO @ Fri, 22 Mar 2019 12:35:37: 6000000

      INFO @ Fri, 22 Mar 2019 12:35:44: 7000000

      INFO @ Fri, 22 Mar 2019 12:35:51: 8000000

      INFO @ Fri, 22 Mar 2019 12:35:57: 9000000

      INFO @ Fri, 22 Mar 2019 12:36:04: 10000000

      INFO @ Fri, 22 Mar 2019 12:36:12: 11000000

      INFO @ Fri, 22 Mar 2019 12:36:19: 12000000

      INFO @ Fri, 22 Mar 2019 12:36:25: 13000000

      INFO @ Fri, 22 Mar 2019 12:36:32: 14000000

      INFO @ Fri, 22 Mar 2019 12:36:39: 15000000

      INFO @ Fri, 22 Mar 2019 12:36:46: 16000000

      INFO @ Fri, 22 Mar 2019 12:36:53: 17000000

      INFO @ Fri, 22 Mar 2019 12:37:01: 18000000

      INFO @ Fri, 22 Mar 2019 12:37:08: 19000000

      INFO @ Fri, 22 Mar 2019 12:37:14: 20000000

      INFO @ Fri, 22 Mar 2019 12:37:21: 21000000

      INFO @ Fri, 22 Mar 2019 12:37:28: 22000000

      INFO @ Fri, 22 Mar 2019 12:37:35: 23000000

      INFO @ Fri, 22 Mar 2019 12:37:42: 24000000

      INFO @ Fri, 22 Mar 2019 12:37:49: 25000000

      INFO @ Fri, 22 Mar 2019 12:37:56: 26000000

      INFO @ Fri, 22 Mar 2019 12:38:04: 27000000

      INFO @ Fri, 22 Mar 2019 12:38:11: 28000000

      INFO @ Fri, 22 Mar 2019 12:38:19: 29000000

      INFO @ Fri, 22 Mar 2019 12:38:28: 30000000

      INFO @ Fri, 22 Mar 2019 12:38:36: 31000000

      INFO @ Fri, 22 Mar 2019 12:39:05: #1.2 read input fragments...

      INFO @ Fri, 22 Mar 2019 12:39:14: 1000000

      INFO @ Fri, 22 Mar 2019 12:39:21: 2000000

      INFO @ Fri, 22 Mar 2019 12:39:27: 3000000

      INFO @ Fri, 22 Mar 2019 12:39:34: 4000000

      INFO @ Fri, 22 Mar 2019 12:39:41: 5000000

      INFO @ Fri, 22 Mar 2019 12:39:48: 6000000

      INFO @ Fri, 22 Mar 2019 12:39:55: 7000000

      INFO @ Fri, 22 Mar 2019 12:40:02: 8000000

      INFO @ Fri, 22 Mar 2019 12:40:09: 9000000

      INFO @ Fri, 22 Mar 2019 12:40:16: 10000000

      INFO @ Fri, 22 Mar 2019 12:40:23: 11000000

      INFO @ Fri, 22 Mar 2019 12:40:30: 12000000

      INFO @ Fri, 22 Mar 2019 12:40:37: 13000000

      INFO @ Fri, 22 Mar 2019 12:40:46: 14000000

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 mean fragment size is determined as 2508.6 bp from treatment

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 note: mean fragment size in control is 2606.8 bp -- value ignored

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 fragment size = 2508.6

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 total fragments in treatment: 31689440

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 user defined the maximum fragments...

      INFO @ Fri, 22 Mar 2019 12:41:02: #1 filter out redundant fragments by allowing at most 1 identical fragment(s)

      INFO @ Fri, 22 Mar 2019 12:41:56: #1 fragments after filtering in treatment: 31667534

      INFO @ Fri, 22 Mar 2019 12:41:56: #1 Redundant rate of treatment: 0.00

      INFO @ Fri, 22 Mar 2019 12:41:56: #1 total fragments in control: 14684539

      INFO @ Fri, 22 Mar 2019 12:41:56: #1 user defined the maximum fragments...

      INFO @ Fri, 22 Mar 2019 12:41:56: #1 filter out redundant fragments by allowing at most 1 identical fragment(s)

      INFO @ Fri, 22 Mar 2019 12:42:22: #1 fragments after filtering in control: 14676434

      INFO @ Fri, 22 Mar 2019 12:42:22: #1 Redundant rate of control: 0.00

      INFO @ Fri, 22 Mar 2019 12:42:22: #1 finished!

      INFO @ Fri, 22 Mar 2019 12:42:22: #2 Build Peak Model...

      INFO @ Fri, 22 Mar 2019 12:42:22: #2 Skipped...

      INFO @ Fri, 22 Mar 2019 12:42:22: #3 Call peaks...

      INFO @ Fri, 22 Mar 2019 12:42:22: #3 Pre-compute pvalue-qvalue table...

      INFO @ Fri, 22 Mar 2019 12:48:42: #3 In the peak calling step, the following will be performed simultaneously:

      INFO @ Fri, 22 Mar 2019 12:48:42: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... myc1_treat_pileup.bdg

      INFO @ Fri, 22 Mar 2019 12:48:42: #3 Write bedGraph files for control lambda (after scaling if necessary)... myc1_control_lambda.bdg

      INFO @ Fri, 22 Mar 2019 12:48:42: #3 Pileup will be based on sequencing depth in control.

      INFO @ Fri, 22 Mar 2019 12:48:42: #3 Call peaks for each chromosome...

      INFO @ Fri, 22 Mar 2019 12:53:34: #4 Write output xls file... myc1_peaks.xls

      INFO @ Fri, 22 Mar 2019 12:53:34: #4 Write peak in narrowPeak format file... myc1_peaks.narrowPeak

      INFO @ Fri, 22 Mar 2019 12:53:35: #4 Write summits bed file... myc1_summits.bed

      INFO @ Fri, 22 Mar 2019 12:53:35: Done!

      Comment

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