en_full_cis_range and en-trans

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Issue #18 resolved
Rola Dali created an issue


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.

Comments (2)

  1. Mikhail Spivakov

    Hi Rola, thanks - good to know you're finding Chicago useful for MUGQIC. I suppose your questions no longer relate to 'issues' in the pipeline, so how about we discuss them by email? mikhail spivakov at babraham ac uk

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