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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Use HiC-Pro allValidPairs as input #28

Open martinaryee opened 7 years ago

martinaryee commented 7 years ago

It would be great to be able to specify a hicpro allValidPairs file as input for hichipper instead of the full hicpro output dir. The other inputs would probably be a restriction fragment bed file and possible a peak set.

This feature would make it easier to put hichipper into a pipeline that runs hicpro as a first step where we only retain a few key output files (e.g. allValidPairs).

rdali commented 6 years ago

It would also be great of it can work with other HiC aligners. We use HiCUP and get a bam file with all the valid reads but that doesnt seem like an option at the moment

werhoog commented 6 years ago

I have the same problem. It is more meaningful to use allValidPairs other than .pairs from the output file of HiC-Pro. But when I tried to discard other pairs file other than allValidPairs file . The screen showed ".*Pairs,no such file or dir" why? So, does this mean hichipper can automaticly knows to use only allValidPairs?Maybe this makes no sense!

Thanks!

TintingLi commented 5 years ago

The latest version of hicpro(2.11.1) change the _allValidPairs to .allValidPairs, which make it uncompatible with hichipper.

caleblareau commented 5 years ago

Thanks for the comment TinTingLi. We’ved push version 0.7.5 (part of a pull request from 0xaf1f) that addresses this.

On Jan 13, 2019, at 3:56 AM, TinTingLi notifications@github.com wrote:

The latest version of hicpro(2.11.1) change the _allValidPairs to .allValidPairs, which make it uncompatible with hichipper.

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liyini0823 commented 5 years ago

I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?

caleblareau commented 5 years ago

Seems like a Hi-C Pro issue rather than a hichipper issue?

On Mar 22, 2019, at 9:31 AM, 旖旎 notifications@github.com wrote:

I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aryeelab/hichipper/issues/28#issuecomment-475621498, or mute the thread https://github.com/notifications/unsubscribe-auth/APei4XhY65EojMULT0ElPMn9zULY7s7hks5vZNszgaJpZM4QdwzT.

TintingLi commented 5 years ago

Dumped reads or dangling reads? These make great difference experimentally speaking.

ting67

ting67@126.com | 签名由网易邮箱大师定制

On 03/22/2019 21:43，Caleb Lareaunotifications@github.com wrote： Seems like a Hi-C Pro issue rather than a hichipper issue?

On Mar 22, 2019, at 9:31 AM, 旖旎 notifications@github.com wrote:

I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aryeelab/hichipper/issues/28#issuecomment-475621498, or mute the thread https://github.com/notifications/unsubscribe-auth/APei4XhY65EojMULT0ElPMn9zULY7s7hks5vZNszgaJpZM4QdwzT.

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