search

mapleforest / HaploMerger2

40 stars 6 forks source link

Reconstructing HM2 haplotypes from original contigs #30

Open mdem7705 opened 3 years ago

mdem7705 commented 3 years ago

Hi there,

I would like to try and reconstruct the haplotypes which were made by Haplomerger2 with my original raw contigs, but I am not sure where to find all of the information.

In the hm.new_scaffolds file I think I can reconstruct each "scaffold_id" by patching together the "start1" and "end1" fields from each contig for the ref haplotype, and "start2" and "end2" fields from each contig for the alt haplotype (please correct me if this is wrong).

My problem is that only 40 scaffolds are represented in this spreadsheet, and I have 118 scaffolds per haplotype. Where can I find information on how the remaining 78 scaffolds were made?

Thank you for your help!

mapleforest commented 3 years ago

You can find them in the file hm.unpaired. If there are still some scaffolds not present in hm.new_scaffolds+hm.unpaired. It would be a problem.

mdem7705 commented 3 years ago

Yes thank you, I found the information I needed.