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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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Phase block and hapdup_phased_{1,2}.fasta #43

Open WeichenZhou opened 2 weeks ago

WeichenZhou commented 2 weeks ago

Hi @mikolmogorov,

Thanks a lot for creating such a great tool! I am new to the genome assembly field. Could you provide some information regarding the relationship between phase block (phased_blocks_hp{1,2}.bed) and hapdupphased{1,2}.fasta? Will the reads from hapdupphased{1,2}.fasta fall into the phase block bed? Or if I have to use the hapdupphased{1,2}.fasta data, should I parse the phase block/set information by myself?

Looking forward to your reply.

Best, Arthur

mikolmogorov commented 1 week ago

Hi Arthur,

In phased_blocks{1,2}.fasta contigs are already split at the phase blocks boundaries. You only need phased_blocks_hp{1,2}.bed if you are working with the dual assembly.

WeichenZhou commented 1 week ago

Hi Mikhail,

Thanks a lot for the reply. What if I observed two contigs that overlapped with each other in aligned phased_blocks{1,2}.fasta? I am not sure how to interpret this.

Best, Arthur