Question

DESeq2 Transcipt Level Support

0

Entering edit mode

andrew.j.skelton73 ▴ 370

@andrewjskelton73-7074

Last seen 8 months ago

United Kingdom

Just out of curiosity, are there any plans for transcript level differential expression (I.e. Supporting fractional counts), with DESeq2??

deseq2 • 882 views

ADD COMMENT • link updated 9.5 years ago by Michael Love 43k • written 9.5 years ago by andrew.j.skelton73 ▴ 370

0

Entering edit mode

Isn't that what DEXSeq is doing?

ADD REPLY • link 9.5 years ago Assa Yeroslaviz ★ 1.5k

0

Entering edit mode

DEXSeq specifically looks specifically at exon usage, rather than differential transcript expression doesn't it?

ADD REPLY • link 9.5 years ago andrew.j.skelton73 ▴ 370

0

Entering edit mode

Yes -- DEXSeq only calls differential expression at the exon level and makes no attempt to "roll up" a transcript level expression estimate.

ADD REPLY • link 9.5 years ago Steve Lianoglou ★ 13k

score 1 · Accepted Answer · 2015-05-13

We don't have current plans to extend beyond gene level. The issue is the estimation variance at transcript level, not the fractional part. This can be very high (much higher than the gene-level expression estimation variance) in cases where, for example, 2 isoforms of a gene differ by only a small region. Here, we recommend the DEXSeq approach.