Good Pipeline for ChIPexo

Question

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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?

[Ben]

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.

Answer 1

[Ming Tommy Tang]

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