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How to properly deal with RefSeq pseudogenes without transcript? #393

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soi opened this issue Apr 6, 2021 · 0 comments
Open

How to properly deal with RefSeq pseudogenes without transcript? #393

soi opened this issue Apr 6, 2021 · 0 comments
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soi commented Apr 6, 2021

In the new refseq human and mouse genomes, there are many pseudogenes annotated with exons but no transcript (makes sense I guess).
The types.py lists pseudogenes as valid super locuses, so how should we deal with that? I added some code that basically throws the exons away, leaving empty genes that are also discarded later, resulting in many error messages.

@soi soi added bug Something isn't working question Further information is requested labels Apr 6, 2021
@soi soi changed the title How to deal with RefSeq Pseudogenes without transcript? How to properly deal with RefSeq pseudogenes without transcript? Apr 6, 2021
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