How to reflect the sequence IDs in final *HiC.fasta file to .assembly and .hic files?
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李允求
Feb 16, 2025, 2:10:27 AMFeb 16
to 3D Genomics
Hi,
In our routine, we always perform optical genome mapping before Hi-C seq, so the files that are output when run-asm-pipeline.sh is run (HiC.fasta, HiC.assembly) are almost always sufficient for final assembly, and we rarely use run-asm-pipeline-post-review.sh.
We realized the IDs of the sequences in *HiC.assembly are different from the IDs in *HiC.fasta. For example, IDs in *HiC.assembly are like "ptg000001l:::fragment_5:::debris".
I would like to visualize the results of 3D-DNA using software such as HiCPlotter.
In our routine, we always perform optical genome mapping before Hi-C seq, so the files that are output when run-asm-pipeline.sh is run (HiC.fasta, HiC.assembly) are almost always sufficient for final assembly, and we rarely use run-asm-pipeline-post-review.sh.
We realized the IDs of the sequences in *HiC.assembly are different from the IDs in *HiC.fasta. For example, IDs in *HiC.assembly are like "ptg000001l:::fragment_5:::debris".
We also realized that *rawchrom.hic file does not contain information of each chromosome or scaffold. When we try to obtain sequence information using hic-straw, it returns the result saying that the entire sequence is treated as a single sequence called "assembly".
How can I reflect the sequence IDs in final *HiC.fasta file to .assembly and .hic files?
Sincerely,
Jung
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