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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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HiC-Pro use with non-reference genomes #313

Closed joeplanta closed 4 years ago

joeplanta commented 4 years ago

Hi,

I am working on non-reference genomes for a few grass species. We do not have chromosome sizes for our assemblies and so can we use HiC-Pro to process our Hi-C data? The HiC-Pro paper used the annotated human genome and the program requires chromosome sizes so I am not sure if we can use HiC-Pro.

Thanks, Jose

nservant commented 4 years ago

Hi Jose, What do you mean by "non-reference genomes" ? If you do not have any reference genome, you should use other software design for de-novo assembly for instance Best

joeplanta commented 4 years ago

Hi Nicolas,

By "non-reference genomes" I mean those that have not been sequenced yet. Thank you. I will check out other programs.