Changes between Version 50 and Version 51 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
03/04/20 11:06:05 (5 years ago)
Author:
thiruvil
Comment:

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  • SOPs/chip_seq_peaks

    v50 v51  
    4949}}}
    5050  * -B create bedgraph output files
    51   * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads).  In BAMPE mode, MACS2 will only use properly-paired read alignments, see [[https://groups.google.com/forum/#!topic/macs-announcement/Vh916L3tOOE | MACS2 Forum ]], also from the readme/manual, "when format BAMPE is specified, MACS will use the real fragments inferred from alignment results for reads pileup."  If you have PE ChIP-Seq data, -f bampe option is recommended.
     51  * -f Input format (typically BAM for single-end reads and BAMPE for paired-end reads).  In BAMPE mode, MACS2 will only use properly-paired read alignments, see [[https://groups.google.com/forum/#!topic/macs-announcement/Vh916L3tOOE | MACS2 Forum ]], also from the readme/manual, "when format BAMPE is specified, MACS will use the real fragments inferred from alignment results for reads pileup.", i.e. --nomodel/--extsize will be ignored.
    5252  * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. By default it means shifting size = 100.                     
    5353  * --extsize When nomodel is true, MACS will use this value as fragment size to extend each read towards 3' end
    54   * --keep-dup How should MACS handle duplicate tags at the same location?  The default is to keep just one.  The 'auto' option (recommended for high-coverage samples) has MACS calculate the expected maximum tags at the same location (based on the binomal distribution).
     54  * --keep-dup How should MACS handle duplicate tags at the same location?  The default is to keep just one.  The 'auto' option (recommended for high-coverage samples) has MACS calculate the expected maximum tags at the same location (based on the binomal distribution).  FastQC results can be used to gauge the duplication levels in a sample.
    5555  * For future IDR analysis, use '-p 1e -3' => Set p-value cutoff to 1e-3 (which is more relaxed than the default setting)
    5656