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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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What is the different between Allele.gene.table and Allele.ctg.table files? #152

Closed sen1019san closed 1 year ago

sen1019san commented 1 year ago

Hi, Zhang. I am trying to assemble haplotype genome using ALLHiC. I am puzzled by the partition.pl step using Allele.gene.table. And I find the alternative partition_gmap.py. So I have two questions:

  1. Is Allele.gene.table and Allele.ctg.table the same thing? I found you mentioned that in run partition.pl error #93. It seems that the two files are different. But I don't know how to get the Allele.gene.table file.
  2. Is the ALLHiC_prune work by using partition.pl outputs? I find the inputs of partition.pl and ALLHiC_prune are quite the same.
sen1019san commented 1 year ago

I have tried to generate these two files by using gmap alignment and a modified python script. Thanks!