Changes between Version 3 and Version 4 of SOPs/InProgressChipSeq


Ignore:
Timestamp:
05/14/14 12:28:38 (11 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/InProgressChipSeq

    v3 v4  
    7474
    7575==== MACS2 ====
     76
     77  * MACS2 is appropriate for both proteins like transcription factors that may have narrow peaks, as well as histone modifications that may affect broader regions. For broader peaks we recommend using --nomodel, --nolambda (if there's no control), and using the fragment size calculated on the strand cross correlation analysis.  We recommend using macs2 rather than macs14 for broad peaks.
    7678{{{
    7779macs2  callpeak -t IP_reads.mapped_only.bam  -c Control_reads.mapped_only.bam -f BAM -g mm  -n Name --nomodel   -B