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Manual
ChiLin is made to be easy. Follow the steps below for a quick start
- Python3 (>= 3.2)
- samflow
- cistrome application package
- pip (install distribute first)
Let us copy and paste the following lines into a conf file, then save it (e.g. hello_chilin.conf).
[Basis]
id =
species =
factor =
treat =
control =
output =
[lib]
genome_index =
chrom_len =
chrom_bed =
gene_table =
dhs =
velcro =
refgene =
phast =
Now you can edit this file and fill the value into the right side of =
After filling all the fields above, you can start running ChiLin now:
ChiLin2.py run -c hello_chilin.conf
Green hand of ChiLin usually wants to try ChiLin in Sandbox mode before running. The Sandbox mode here means that ChiLin will output the information of whole workflow (every shell commands), but doesn't process these commands actually. In one word, it pretends to run ChiLin but doesn't run actually. Still confused? Just give it a try like this:
ChiLin2.py run -c hello_chilin.conf --dry-run
The workflow of ChiLin is consisted of the following steps:
- Groom Raw Sequencing Files
- Quality Control (QC) for Raw Sequencing Files using FastQC
- Library Contamination Detection
- Reads Mapping and QC using Bowtie
- Peak Calling and QC for datasets using MACS2
- Peak Calling and QC for replicates using MACS2
- Venn Diagram of peaks for replicates
- Correlation of Signals for replicates
- Overlapping of DnaseI Sensitive Sites (DHS) and QC
- Overlapping of velcro regions (blacklist) and QC
- Annotation Statistics using CEAS
- Conservation Statistics with PhastCons
- Motif Analysis using MDSeqPos
Sometimes you might want to skip a few unimportant steps, for example, skip Motif Analysis for a H3K4me3 data. Then you can do like this:
ChiLin2.py --run -c hello_chilin.conf --to 12
Or like this:
ChiLin2.py --run -c hello_chilin.conf --skip 13
The two commands are actually equivalent.
To be continued