aryeelab
Use HiC-Pro allValidPairs as input
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).
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
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!
The latest version of hicpro(2.11.1) change the *_allValidPairs to *.allValidPairs, which make it uncompatible with hichipper.
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 [email protected] wrote:
The latest version of hicpro(2.11.1) change the *_allValidPairs to *.allValidPairs, which make it uncompatible with hichipper.
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I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?
Seems like a Hi-C Pro issue rather than a hichipper issue?
On Mar 22, 2019, at 9:31 AM, 旖旎 [email protected] wrote:
I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?
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Dumped reads or dangling reads? These make great difference experimentally speaking.
| | ting67 | | [email protected] | 签名由网易邮箱大师定制
On 03/22/2019 21:43，Caleb Lareau[email protected] wrote： Seems like a Hi-C Pro issue rather than a hichipper issue?
On Mar 22, 2019, at 9:31 AM, 旖旎 [email protected] wrote:
I run HiC-Pro and get too many Dumped reads rather than Valid paired. I want to down why ?
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