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How does one define inputs for TreeValGal? #554

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nekrut opened this issue Oct 8, 2024 · 1 comment
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How does one define inputs for TreeValGal? #554

nekrut opened this issue Oct 8, 2024 · 1 comment
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@Delphine-L

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@nekrut
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nekrut commented Oct 8, 2024 •
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A clear procedure needs to be developed to gather inputs to run each new assembly:

  • Two assembled haplotypes (same contig names);
  • Optional NCBI gene/rna/protein taxon id and downloaded fasta files;
  • Optional haplotype or reference fasta from two or more closely related species for sequence similarity mapping;
  • Run repeatmodeler for repeatmasker if both can be made to work;
@nekrut nekrut converted this from a draft issue Oct 8, 2024
@fubar2
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fubar2 commented Oct 9, 2024 •
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FWIW: Draft documentation includes some notes on inputs and the IWC PR is in.

Basic tracks:

Dimers, coverage, SV:

@Delphine-L Delphine-L moved this from Todo to Done in TreeValGal / EGAPx tasks Dec 11, 2024
@Delphine-L Delphine-L closed this as completed by moving to Done in TreeValGal / EGAPx tasks Dec 11, 2024
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