search

GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
132 stars 22 forks source link

Run data prep with --genome flag #44

Closed callumparr closed 3 years ago

callumparr commented 3 years ago

I was confused if and why --genome flag is needed if we run the initial mapping and eventalign using transcriptome.

I did not add and now I read another issue here where someone asked if adding --genome flag is wrong. Now I worry all that time I ran it for is wasted. If --genome flag is expected why is it as default? Sorry for so many questions.

A little confused.

ploy-np commented 3 years ago

If you want to detect differential modification per genomic position, you need to put --genome flag in the xpore-dataprep command. It will model all transcripts aligned to the same genomic position together. But if you want to detect differential modification per transcriptomic position, you don't need to use this flag.

callumparr commented 3 years ago

Ah I see. Thank you that makes sense. So event align is done in transcriptome space and then dataprep can either stick with transcriptome or workback to genomic coordinates?