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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 without reference genome #404

Closed B10inform closed 3 years ago

B10inform commented 3 years ago

Hi,

Can HiC-Pro work without a reference genome? How distant genome (similar species) can work as a reference genome?

Thanks

nservant commented 3 years ago

Hi No, HiC-Pro requires a reference genome. What do you mean by distant genome ? not sure to see your point ? N

B10inform commented 3 years ago

I meant if Rubus occidentalis (black raspbarry) could be used as reference for Rubus idaeus (red raspberry).

nservant commented 3 years ago

Well, this is up to you ! I have no idea how different are these reference genomes. This is a general question which is also true when we are working with human, mouse, etc. How different are our genome from the reference ? In practice, you can still modify the bowtie2 parameters if you want to be a bit more flexible in the mapping. best

kishor2019 commented 3 years ago

Hi @nservant can you please tell about the quality of the of reference genome? Beaucse in my case i want to make a denovo assembly of a fish genome. In that case, the closest reference species is from another genus and it was also not in chromosome level. If i want to seek for chromosome level reference assembly i need to go for Danio which is little bit far, actually a diiferent family. So it will be helpful for me if i get some idea about selecting reference species (in context of distance as well as in context of quality of assembly).

nservant commented 3 years ago

Hi, Well, for sure the more different your reference genome is from your real data, the more complicated will be the reads mapping. If you think your genome is too divergent from Danio, you should not use it. One thing you could do would be to use your Hi-C data for genome assembly. HiC-Pro is not designed for that, but there are other tools dedicated to this question. Best

kishor2019 commented 3 years ago

Thanks.

On Fri, Apr 9, 2021, 21:07 Nicolas Servant @.***> wrote:

Hi, Well, for sure the more different your reference genome is from your real data, the more complicated will be the reads mapping. If you think your genome is too divergent from Danio, you should not use it. One thing you could do would be to use your Hi-C data for genome assembly. HiC-Pro is not designed for that, but there are other tools dedicated to this question. Best

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