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estepi / ASpli

Analysis of alternative splicing using RNAseq
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dots in chromosome names lead errors #2

Open andreasleha opened 6 years ago

andreasleha commented 6 years ago

Dots in chromosome names (such as AABR07024104.1) lead to the error

Error in data.frame(matrix(unlist(strsplit(jnames, "[.]")), byrow = TRUE,  : 
  row names supplied are of the wrong length

within the .createGRangesExpJunctions function.

This is triggered via junctionDUreport, e.g.

estepi commented 6 years ago

Hi, Yes. If the chromosome name has a dot, it causes this problem Can you avoid this notation? (For example, replacing with a "-", "_" or nothing.) I can help with this if you need. Cheers, Estefi

andreasleha commented 6 years ago

Thanks. I am fine.

I opened this report more as a feature request that ASpli should be able to handle this situation or at least give an explicit error earlier on in the pipeline about not being able to handle such names.

estepi commented 6 years ago

Yes, you're completely right. We are trying to fix it in order not to depend on annotation format.

andreasleha commented 6 years ago

Thanks for the immediate reaction to this issue. Impressive