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Changes between Version 11 and Version 12 of SOPs/chip_seq_peaks

v11	v12
79	79	==== MACS2 ====
80	80
81		* 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. Identifying reproducible peaks (across replicates) with IDR requires MACS2 and works best with a relaxed p-value threshold.
	81	* 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,--broad, --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. Identifying reproducible peaks (across replicates) with IDR requires MACS2 and works best with a relaxed p-value threshold.
82	82	{{{
83	83	bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name --nomodel -B