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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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Pruning step after assigning contigs into homologous groups #131

Closed Huyuxi08 closed 2 years ago

Huyuxi08 commented 2 years ago

Hi @tangerzhang,

As you mentioned in https://github.com/tangerzhang/ALLHiC/issues/93, after generating the wrk_dir directory with the script partition_gmap.pl, ALLHiC_prune can be executed individually in each folder with the same Allele.ctg.table. Following your genome assembly script for sugarcane, I'm a little confused about this command： ALLHiC_prune -i Allele.ctg.table -b sample.clean.bam -r seq.fasta. Should the sample.clean.bam in this command use the prunning.sub.bam generated by partition_gmap.pl or the whole sample.clean.bam previously generated with samtools?

Thanks a lot!

kedduck commented 1 year ago

I meet the same problem, could you please share the solution? @Huyuxi08

Huyuxi08 commented 1 year ago

@kedduck Hi, you should use the prunning.sub.bam generated by partition_gmap.pl.

kedduck commented 1 year ago

Thanks for your relpy!