Changes between Version 13 and Version 14 of SOPs/InProgress


Ignore:
Timestamp:
05/13/14 17:58:01 (11 years ago)
Author:
byuan
Comment:

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  • SOPs/InProgress

    v13 v14  
    11Get reproducible peaks from multiple chip-seq replicates with IDR (https://sites.google.com/site/anshulkundaje/projects/idr)
    22
    3 # use macs2 to get peaks: You can use --nomodel --shiftsize fragmentLenth based on NSC/RSC
    4 bsub macs2 callpeak -t IP_1.bam -c control_1.bam  -f BAM -g hs -n IP.1_vs_control.1 -B  -p 1e-3
    5 bsub macs2 callpeak -t IP_2.bam -c control_2.bam  -f BAM -g hs -n IP.2_vs_control.2 -B  -p 1e-3
     3== use macs2 to get peaks: You can adjust fragment length with --nomodel --shiftsize if NSC/RSC plots are not good ==
     4* bsub macs2 callpeak -t IP_1.bam -c control_1.bam  -f BAM -g hs -n IP.1_vs_control.1 -B  -p 1e-3
     5* bsub macs2 callpeak -t IP_2.bam -c control_2.bam  -f BAM -g hs -n IP.2_vs_control.2 -B  -p 1e-3
    66
    7 # sort .narrowPeak files ( macs2 output) from best to worst using the -log10(pvalue) column i.e. column 8, and only keep the top 100k peaks
     7== sort .narrowPeak files ( macs2 output) from best to worst using the -log10(pvalue) column i.e. column 8, and only keep the top 100k peaks ==
    88bsub "sort -k 8nr,8nr IP.1_vs_control.1_peaks.narrowPeak |head -n 100000|gzip -c >| IP.1_vs_control.1.regionPeak.gz"
    99bsub "sort -k 8nr,8nr IP.2_vs_control.2_peaks.narrowPeak |head -n 100000|gzip -c >| IP.2_vs_control.2.regionPeak.gz"