How to run the diploid portion of the pipeline to identify/remove alternative haplotypes if i want a haploid representation of the hybrid genome

theaidenlab / AGWG-merge

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How to run the diploid portion of the pipeline to identify/remove alternative haplotypes if i want a haploid representation of the hybrid genome #1

Open Xuelei-Dai opened 5 years ago

Xuelei-Dai commented 5 years ago

Hello, I want to run the diploid portion of the pipeline to identify/remove alternative haplotypes if i want a haploid representation of the hybrid genome,should I run the awk -f ${path_to_3ddna}/utils/generate-assembly-file-from-fasta.awk AGWG.draft.fasta > AGWG.draft.assembly command and remove undercollapsed heterozygosity,finaly,run ofhaploid of 3d-dna . http://www.aidenlab.org/forum.html?place=msg%2F3d-genomics%2FKzQW9s8awTk%2FkcvpQVFlAAAJ

Thank you

dudcha commented 5 years ago

Hello fastasticair,

Running haploid mode of 3D-DNA does not require you to generate an assembly file beforehand. See -h|--help in 3D-DNA for instructions how to run the full pipeline or fast-forward to merge by invoking -s merge.

Best, Olga