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hwlim / BisKit-RNA

BisKit for CCHMC HPC users
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splicingin alignment to RNA reference #5

Closed hwlim closed 4 months ago

hwlim commented 5 months ago

There are substantial spliced alignment. Should we prevent spliced alignment in non-genomic alignment? Does hisat2-3n has that type of options?

cahn20 commented 5 months ago

There is a flag in hisat-3n called "--no-spliced-alignment".

I'm surprised that splicing is even done for RNA though; I thought we had to specifically provide a custom index generated by HISAT using "hisat-3n-build" by including known splice site information (which I did only for the genome index). I guess the alignment step doesn't recognize the index itself.

I can add two additional parameters to the config.bis.yml file which will be transferred to the rule.smk file:

  1. Allow_genome_spliced_alignment
    • Setting this to True would allow spliced alignment for the genome; default = TRUE
  2. Allow_RNA_spliced_alignment
    • Setting this to True would allow spliced alignment for RNA; default = FALSE
cahn20 commented 4 months ago

This is fixed in pull request https://github.com/hwlim/BisKit_CCHMC/pull/6 (already merged).