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Multiome: Generate chromosome length from fasta files. #1285

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Bento007 opened this issue Mar 5, 2025 · 0 comments
Open

Multiome: Generate chromosome length from fasta files. #1285

Bento007 opened this issue Mar 5, 2025 · 0 comments

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@Bento007
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Bento007 commented Mar 5, 2025

currently the chromosome table for both mouse and human are hardcoded into the atac_seq.py. This will eventually become problematic when it's time to update the gencode version. This process should be automated when ever gencode version are updated.

# TODO: these chromosome tables should be calculated from the fasta file?
# location of fasta https://www.gencodegenes.org/human/release_44.html and file name GRCh38.primary_assembly.genome.fa

DoD

The chromosome lengths are generate from a fasta file from gencode and usable by the atac validation code.

@brianraymor brianraymor changed the title Generate chromosome length from fasta files. Multiome: Generate chromosome length from fasta files. Mar 5, 2025
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