exclude read for HiC scaffolding

[baozg]

Hello, @arangrhie

In the VGP preprint, you use exclude_read.sh for binning the HiC reads. But in my trio project, we only have child hifi reads and parents Illumina reads.

So can I just use the paternal or maternal spciefic reads or using HiFi kmer to get hapmer?

Thanks, Zhigui Bao

[arangrhie]

Hi @baozg ,

Yes, you could try the hapmer.sh using HiFi kmer if that is your only option for the child. Then, use the hapmers with the exclude_reads.sh to exclude reads with one haplotype from your hi-C reads.

Thanks, Arang

[baozg]

Thank for the promptly repsone, I will try hapmer.