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ChiLin

ChiLin is a pipeline for ChIP-seq data written in pure Python. It provides workflow of mapping(Bowtie), peak calling(MACS2), Cis-elementary visualization(CEAS) and motif finding(MDSeqpos). Moreover, it provides quality control tools for reads, replication and peaks. It's intended to do more things with less configuration.

Nutshell

Here is a workflow of using ChiLin:

1. type in this command to generate a config file:

ChiLin gen -s hg19 > a_meaningful_name.conf

2. modify the basis part to meet your requirement
   [basis]
   user = foo
   id = 2012
   time = 2102xxx
   species = {{ species }}
   factor = ESR1
   treat = absolutepath
   control = absolutepath
   output = absolutepath
3. run the analysis part
   ChiLin run -c a_meaningful_name.conf -t TF(orHistone)