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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

Input format #11

Closed Phlya closed 5 years ago

Phlya commented 5 years ago

Hi! This tools looks really interesting and I would like to give it a try. Is it possible to make input format more flexible? E.g. support the .pairs format from 4DN, and its extension from the Mirny? https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md lab https://pairtools.readthedocs.io/en/latest/formats.html

Or allow specification of which column in the data corresponds to what...

Converting such huge files takes a long time, considering they need to by un-gzipped and then gzipped agian. Thank you!

YaqiangCao commented 5 years ago

Hi Ilya, Thanks for your interest in cLoops, and it is quite a good suggestion to support more popular and flexible input data format. However, I am current focusing on improving the algorithm as support more kinds of data, such as Capture-HiC, and more accurate loop calling related work, which should be more important to the general users. Thanks again for the suggestions. I will let you know when we do the updates. Thanks. Yaqiang

On Tue, Aug 6, 2019 at 7:17 AM Ilya Flyamer notifications@github.com wrote:

Hi! This tools looks really interesting and I would like to give it a try. Is it possible to make input format more flexible? E.g. support the .pairs format from 4DN, and its extension from the Mirny?

https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md lab https://pairtools.readthedocs.io/en/latest/formats.html

Or allow specification of which column in the data corresponds to what...

Converting such huge files takes a long time, considering they need to by un-gzipped and then gzipped agian. Thank you!

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