Question

remving pseudogenes and lncRNA from deseq2 res

0

Entering edit mode

PD • 0

@882813fa

Last seen 19 months ago

Australia

Hi I would like to exclude lncrna and pseuodogens from DEG results (using DESeq2). At what step do I do this? Thanks

```

filter deseq2 • 975 views

ADD COMMENT • link updated 19 months ago by Michael Love 43k • written 19 months ago by PD • 0

score 0 · Answer 1 · 2023-04-21

0

Entering edit mode

Michael Love 43k

@mikelove

Last seen 1 day ago

United States

This is up to you. You could do this at the beginning, before running DESeq().

ADD COMMENT • link 19 months ago Michael Love 43k

0

Entering edit mode

Thanks Michael. Can you share a code to do this please?

ADD REPLY • link 19 months ago PD • 0

0

Entering edit mode

I don't have any particular code on hand, I don't actually exclude these features. There are various source of annotation available within Bioconductor.

ADD REPLY • link 19 months ago Michael Love 43k