ChromIntNet

Converts ChIA-PET paired format to Cytoscape compatible SIF and edge attribute files

Input format

Paired form from ChIA-PET

Name chrom1 start1 end1 chrom2 start2 end2 score

mkdir <outputFolder>
python2.7 ChromIntNet.py --cluster-prefix <pref> <input> <outputFolder>/

Cytoscape compatible SIF file and edge attributes (tab delimited) In the / SIF file clusterNet.sif

<pref>_<N1> ChIAPETLoop <pref>_<N2>

Edge attribute file clusterNet.edgeAttrs.txt where interaction strength = sum of scores for all ChIA-PET pairs with tags in each cluster.

<pref>_<N1> (ChIAPETLoop) <pref>_<N2> <interaction_strength>

Interval file for the clusters clusters.bed where numTags is the number of tags clustered together

<chrom> <start> <end> <pref>_<N> <numTags>

Tag interval file nodes.bed where name = _/ where Name is from the original ChIA-PET input

<chrom> <start> <end> <pref>_<N>/<Name>