Question: Good Pipeline for ChIPexo
0
gravatar for ad
3.0 years ago by
ad30
United States
ad30 wrote:

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?

ADD COMMENTlink modified 3.0 years ago by Ming Tang2.6k • written 3.0 years ago by ad30

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 REPLYlink written 3.0 years ago by Ben50
0
gravatar for Ming Tang
3.0 years ago by
Ming Tang2.6k
Houston/MD Anderson Cancer Center
Ming Tang2.6k wrote:

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

ADD COMMENTlink written 3.0 years ago by Ming Tang2.6k
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