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YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.
https://yaqiangcao.github.io/cLoops/
MIT License
109 stars 17 forks source link

using cloops from Juicer #29

Closed yamzaleg closed 3 years ago

yamzaleg commented 3 years ago

Hello I used Juicer to preprocess my data and make .hic files. I am trying to use different loop calling tools to get a sense of what are the most confident loops in my dataset. I know that the input files for cLoops are .bedpe files, I'm wondering if you have a pipeline from Juicer to cloops.

If you don't, I'm wondering how you pre-process the fastq files prior to running cLoops.

Thank you so much,

Yonatan

YaqiangCao commented 3 years ago

Please refer to Hic-Pro for pre-processing, the a script in cLoops called hicpropairs2bedpe can be used. Good luck.

yamzaleg @.***>于2021年7月2日 周五下午3:14写道：

Hello I used Juicer to preprocess my data and make .hic files. I am trying to use different loop calling tools to get a sense of what are the most confident loops in my dataset. I know that the input files for cLoops are .bedpe files, I'm wondering if you have a pipeline from Juicer to cloops.

If you don't, I'm wondering how you pre-process the fastq files prior to running cLoops.

Thank you so much,

Yonatan

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yamzaleg commented 3 years ago

Thank you so much for your reply. As I have already aligned the files using Juicer, is there a way to convert one of the output files to something I can use in cLoops? (I know you probably can't convert a .hic to a .bedpe file).

Thank you again, Yonatan