Good Pipeline for ChIPexo
1
0
Entering edit mode
5.2 years ago
ad ▴ 30

Hello, I was wondering what was an ideal or the 'standard' pipeline for chipexo. Would something like raw seq results->fastq files->Bowtie for alignment -> GEM for peakcalling be good? Will this provide good 'enduser' data for the experimental scientist or is there another standard processing step? Would bowtie2 be better than bowtie?

ChIP-Seq alignment sequence next-gen • 864 views
ADD COMMENT
0
Entering edit mode

yes, the goal of ChIPexo is to obtain peak. So you just align the clean reads into reference genome and do peak calling using some softwares.

ADD REPLY
0
Entering edit mode
5.2 years ago
Ming Tang ★ 2.7k

bowtie2 is for reads longer than 50bp if you have short reads such as 36 bp use bowtie1

ADD COMMENT

Login before adding your answer.

Traffic: 697 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6