Question

remving pseudogenes and lncRNA from deseq2 res

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PD • 0

@882813fa

Last seen 18 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

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filter deseq2 • 968 views

ADD COMMENT • link updated 19 months ago by Michael Love 42k • written 19 months ago by PD • 0

score 0 · Answer 1 · 2023-04-21

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Michael Love 42k

@mikelove

Last seen 5 hours 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 42k

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

ADD REPLY • link 19 months ago PD • 0

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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 42k