SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
macs2 -- peak calling error on non-model genome grgmncr Bioinformatics 0 07-29-2014 11:08 AM
Small RNA library: 30nt peak? Erlkoenig RNA Sequencing 1 05-09-2014 01:07 PM
Identification of microRNA peak from Agilent samll RNA ship jinpingzhang SOLiD 0 08-14-2012 05:36 PM
small RNA sample peak at 16nt? vebaev RNA Sequencing 1 07-02-2012 01:27 AM

Reply
 
Thread Tools
Old 05-11-2015, 08:12 AM   #1
skingan
Member
 
Location: San Mateo, CA

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

Hello,

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?

Thanks!
skingan is offline   Reply With Quote
Reply

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

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:09 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO