about the same_fragment filter in hicBuildMatrix

Jiang Xu

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Oct 27, 2019, 8:22:17 PM10/27/19

to deepTools

Hey deepTools people,

I've been using hicExplorer recently. I am a little bit confused about the statics in the QC table,

I found that most of the pairs that are discarded because of the pairs are within 800bp of distance(same fragment). So, is it possible to turn off this filter?

Thanks a lot!

Best!

Jiang

Lin Chen's Lab

Department of Biological Sciences, Computational and Molecular Biology

University of Southern California

Vivek Bhardwaj

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Oct 28, 2019, 8:36:33 AM10/28/19

to Jiang Xu, deepTools

Hi Jiang

These are normal paired-end reads with no restriction site in between them (if you are using RE). They are not considered valid HiC pairs. AFAIK we don't provide an option in hicBuildmatrix to turn it off.

Best Wishes

Vivek

--------

Vivek Bhardwaj

Post-doc Researcher

Hubrecht Institute

3584CT Utrecht

The Netherlands

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jiang

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Oct 28, 2019, 10:10:56 AM10/28/19

to Vivek Bhardwaj, deepTools

Hi Vivek,

Thank you for your explanation. If I didn’t set the RE option? What restriction site will the program look for?

Best!

Jiang

Sent from my iPhone

On Oct 28, 2019, at 5:36 AM, Vivek Bhardwaj <vbhard...@gmail.com> wrote:

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