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maiziezhoulab / RegionIndel

Large indel detection in region-based phased diploid assemblies from linked-reads
MIT License
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human data only? #3

Open pdimens opened 3 months ago

pdimens commented 3 months ago

Hello,

I see that the chr_num parameter excepts only an integer and that the code then expects the contigs to be named chr_. Could this not be generalized to all species if chr_num was just chr as a string and the code then used >chr (etc.) to pull out the relevant contig name?

maiziex commented 2 months ago

Yes, you can. Ensure that the chromosome names in the reference genome FASTA file follow this format.

maiziex commented 2 months ago

Yes, you can. Ensure that the chromosome names in the reference genome FASTA file follow this format.

- Maizie (Xin) Zhou, Ph.D. Assistant Professor Biomedical Engineering, Computer Science, and Data Science Institute Vanderbilt University

5919 Stevenson Center

Nashville, TN 37235

Cell: 336-473-3540

https://lab.vanderbilt.edu/maizie-zhou-lab/

From: Pavel V. Dimens @.> Sent: Friday, July 5, 2024 8:27 AM To: maiziezhoulab/RegionIndel @.> Cc: Subscribed @.***> Subject: [maiziezhoulab/RegionIndel] human data only? (Issue #3)

Hello,

I see that the chrnum parameter excepts only an integer and that the code then expects the contigs to be named chr. Could this not be generalized to all species if chr_num was just chr as a string and the code then used >chr (etc.) to pull out the relevant contig name?

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pdimens commented 2 months ago

Would it not be possible to modify the logic such that the user inputs the full contig/chromosome name rather than forcing Contig names to be chr_ ?

maiziex commented 2 months ago

Unfortunately, some parts of the code logic need to be modified to accommodate this. The easiest approach for now is to modify the contig name. We plan to make this applicable to a general case in a future version.

- Maizie (Xin) Zhou, Ph.D. Assistant Professor Biomedical Engineering, Computer Science, and Data Science Institute Vanderbilt University

5919 Stevenson Center

Nashville, TN 37235

Cell: 336-473-3540

https://lab.vanderbilt.edu/maizie-zhou-lab/

From: Pavel V. Dimens @.> Sent: Tuesday, July 9, 2024 6:48 AM To: maiziezhoulab/RegionIndel @.> Cc: Zhou, Maizie @.>; Comment @.> Subject: Re: [maiziezhoulab/RegionIndel] human data only? (Issue #3)

Would it not be possible to modify the logic such that the user inputs the full contig/chromosome name rather than forcing Contig names to be chr_ ?

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