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Comparison of Hi-C Experiments using Structural Similarity.
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BEDPE file format #37

Closed ysora closed 3 years ago

ysora commented 3 years ago

Hi, I am trying to run chess sim command. In 'pairs' option, I tried to input hiccups output which is composed of 6 columns (chr1, start1, end1, chr2, start2, end2). However, an error occurred saying a file with 10 columns is expected. Could you let me know the exact file format for pairs option in chess sim command? Thanks.

liz-is commented 3 years ago

Hello,

The input BEDPE file should correspond to the format as defined by bedtools. The "score" column is not used and can be a dummy value, but the other columns are required. I thought this was mentioned in the docs but I can't find it, so we can add it / make it more obvious!

However, as discussed in another issue, it sounds like you are trying to use off-diagonal regions as input to CHESS. Unfortunately this will not work properly, as CHESS was designed to work with and tested on regions along the diagonal. To compare loops between samples, you could create windows that include the whole span of the loop, or use a "genome scan" approach as described in the paper.

liz-is commented 3 years ago

Hello, I've now updated the docs and FAQ to address both the expected BEDPE format and the use of off-diagonal regions as input. Do you have any follow up queries? If not, I'll close this issue.

ysora commented 3 years ago

Yes you can close the issue Thanks

Sora

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From: Liz Ing-Simmons notifications@github.com Sent: Monday, March 1, 2021 12:29:17 PM To: vaquerizaslab/chess chess@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [vaquerizaslab/chess] BEDPE file format (#37)

Hello, I've now updated the docshttps://chess-hic.readthedocs.io/en/latest/cli.html#chess-sim and FAQhttps://chess-hic.readthedocs.io/en/latest/faq.html#can-i-use-chess-to-compare-the-results-of-loop-calling-software-between-samples to address both the expected BEDPE format and the use of off-diagonal regions as input. Do you have any follow up queries? If not, I'll close this issue.

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