supply pairs of genomic coordinates for which quimeric reads are simulated

[jazberna1]

Hello FreeHiC developers,

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

Many thanks
Jorge

[yezhengSTAT]

Hello Jorge,
Generally speaking, I don't see any problem with including any quimeric reads for simulation but be careful about post-simulation processing steps where these reads may be filtered out. We are also developing a fast version only based on the genomic coordinates of reads without additional filtering (https://github.com/BaconZhou/FreeHiCLite). You may also give it a try.

Thanks,
Ye

[jazberna1]

Hello Yen,

Many thanks for replying.

I meant if could add a file with pairs of coordinates for which FreeHiC would create significant quimeric reads. Is that what FreeHiC does?

Regards
Jorge

[yezhengSTAT]

What do you mean by quimeric reads? Do you mean chimeric reads? FreeHi-C can simulate a very similar contact matrix from the target contact matrix. More details please refer to https://www.nature.com/articles/s41592-019-0624-3?proof=t.

Thanks,
Ye

[jazberna1]

Hello Ye,

Yes, sorry my bad, I meant chimeric reads.

Jorge