Proximo Hi-C (Phase Genomics)

Question

Proximo Hi-C (Phase Genomics)

Closed this issue 3 years ago · 3 comments

carolhsb commented 4 years ago

Hello,

I have Hi-C data that was constructed with Proximo Hi-C Kit (Phase Genomics). Can I use this data in Salsa?

Thanks in advance,

Carol

Answer 1 · 2021-07-13T20:43:36.000Z

You can use Phase Genomics HiC data normally. I have good results using Arima Genomics mapping pipeline or using bwa and samblast only. For example:
bwa mem -5SP [assembly.fasta] [fwd_hic.fastq] [rev_hic.fastq] | samblaster | samtools view -S -h -b -F 2316 > [aligned.bam]

Answer 2 · 2021-07-13T20:55:50.000Z

Hi,

thanks!
I've used with Arima Genomics mapping pipeline too, and it worked.

Answer 3 · 2022-02-17T00:09:28.000Z

hi @carolhsb or @amvarani - would you mind sharing info on genome size and no mapped HiC reads - I'm seeing zero improvement in my assembly and trying to troubleshoot.