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cerebis / sim3C

Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
GNU General Public License v3.0
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Allow users to prescriptively modulate the interaction rates for specific coordinate pairs. #19

Open jazberna1 opened 3 years ago

jazberna1 commented 3 years ago

Hello sim3C developers,

This is not an issue. I would to know if sim3C can take pairs of genomic coordinates for which quimeric reads are also simulated.

Many thanks Jorge

cerebis commented 3 years ago

Hi Jorge,

I am not quite sure I understand. Sim3C does produce chimeric reads (read-through), if that is what you are asking.

jazberna1 commented 3 years ago

Hello Matthew,

I was wondering If could diffrerentialy boost the contacts between particular pairs of regions of a chromosome. I suppose I could additionally run Sim3C on them and add those resulting reads to those rendered by Sim3C on the whole chromosome. Does that make sense?

Many thanks Jorge

cerebis commented 3 years ago

Unforuntely, there is no facility in sim3C to modulate the frequency of interaction at specific loci. That sounds like an interesting feature though, if you would like to raise an issue with this is a suggestion.

Apologies for the slow reply, my github notification was buried by my email client.

cerebis commented 3 years ago

Actually, lets just modify this issue.