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non-standard chromosome names #19

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pna059 opened this issue Sep 27, 2023 · 1 comment
Open

non-standard chromosome names #19

pna059 opened this issue Sep 27, 2023 · 1 comment
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help wanted Extra attention is needed

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@pna059
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pna059 commented Sep 27, 2023 •
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Hi, our assembly contains chromosomes labeled as chr1H to 7H and chrUn. I use HiC-Pro data format. How shal I modify the sparse matrix to achieve smooth analysis?
Could I just replace all chr names with numbers only in the initial BED file before reading and converting into the sparse matrix?

Thank you!

Pavla
@mdozmorov
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Marking this as a feature for improvement. Currently, we have chromosome names hardcoded as chr1 etc.

Sorry I missed the email about this issue.

@mdozmorov mdozmorov added the help wanted Extra attention is needed label Apr 7, 2024
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@mdozmorov @pna059