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Old 05-11-2015, 08:12 AM   #1
Location: San Mateo, CA

Join Date: Feb 2010
Posts: 17
Default peak identification with macs2 for small RNA data


I have illumina data from small RNAs and am using MACS2 to identify peaks in read mapping. (Read mapping done with bowtie1.) This method was developed for ChIP-Seq so I need to tweak the program settings for my purposes. My command is this:

macs2 callpeak -t mydata.bam -f BAM -g dm -s 29 --keep-dup all --nomodel --bw 15

I am using the nomodel setting to omit the peak shift model. Also set my tag length to 29 and bandwidth to 15. The peaks are still much wider than I expect, 200-300bp instead of 22-29bp.

Any thoughts on the program setting, or recommendations for a more appropriate method?

skingan is offline   Reply With Quote

macs, peak calling, peak length, small rna-seq

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