I have a couple of more clarifications concerning chicago:
1- I have been running chicago through the runChicago.R wrapper, using default parameters.
#! runChicago.R -e seqMonk,interBed,washU_text,washU_track --export-order score --design-dir input_files input_files/sample_HiC/sample_HiC.chinput chicago_output
However, looking through the available parameters, I find
#! --en-full-cis-range --en-trans --en-full-cis-range Assess the enrichment for features for the full distance range [same chromosome only; use --en-trans in addition to include trans-interactions] (can be very slow!) --en-trans Include trans-interactions into enrichment analysis
potentially interesting but I am not sure I fully understand what they do. what does "full distance range" mean? does chicago by default look at only a set distance between bait and target? I ran a test set with and without the parameters. The plots came out exactly the same but the output.ibed had differences in predictions. I just wanted to know what to expect and which one do you recommend.
2- reading your manuscript, I was really interested in the GWAS overlap done with the significant interactions. However, unlike the feature enrichment which is a module in chicago, GWAS enrichment wasn't. Did you just overlap a list of GWAS SNPs with significant reads by genomic overlaps? Can you please elaborate on that since I would like to replicate it as well.
Thank you very much for all the help!
We are trying to use chicago as part of a capture hic pipeline we are building for the genomics community (MUGQIC http://www.computationalgenomics.ca/tools/). So I wanted to make sure I understand the parameters to document them well.