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CraigIDent / SpliSER

Bioinformatic tool for Splice site Strength Estimation using RNA-seq
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Splice donor or splice acceptor?? #3

Closed shiro-kur closed 7 months ago

shiro-kur commented 1 year ago

Hi !

Can I get information on splice donor or acceptor for each splice site from the SpliSER process output?

CraigIDent commented 1 year ago

Hi shiro-kur, Yes you can work this out just using the SpliSER process output, although it requires some scripting or work in excel. The key bit of information is in the list of partners for a given site (in column 11). Partner sites will either be all upstream or all downstream of the site. You can then work out whether a site is donor or acceptor in a couple of ways:

  1. If you have stranded data.

    • A plus (+) strand site with downstream partners (ie all partners have larger position values) must be a splice donor.
    • A plus strand site with upstream partners (ie all partners have smaller position values) must be a splice acceptor.
    • vice versa for minus (-) strand sites

  2. If you have a gene annotation.

    • If a site is within a plus strand gene and has downstream partners, then it is likely a donor site. And so on.

However this second approach will fail when you have sites within overlapping genes. Whatever you do, look at a few known genes in IGV to sanity-check your results.

Hope this helps! Sorry that I didn't see this sooner, Craig