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7.6 years ago
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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?
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.