NeoChiLin /

Filename Size Date modified Message
183 B
147 B
705 B
7.8 KB
873 B
1.2 KB


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.


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
   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)
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.