Using IsoQuant counts with DESeq2?

[gaoxiangcao]

Hi, thanks for the great tool! Can I use the transcript-level counts from IsoQuant as input for DESeq2 for differential expression analysis? Thanks!

[andrewprzh]

Dear @gaoxiangcao

Yes, I don't see any reasons why not. Just keep in mind that compared to short reads, long reads don't require gene length normalization when counting TPMs or other normalized values.

Best Andrey

[gaoxiangcao]

Dear Andrey,

Thanks for the reminder! Yes, as far as I understand, DESeq2 does not perform gene length normalization by default.

Best, Gaoxiang

[sagnikbanerjee15]

Hello @andrewprzh,

While reporting TPM values does isoquant normalize only on sequencing depth. Could you please confirm that it does not normalize on gene/transcript length?

Thanks Sagnik

[andrewprzh]

Dear @sagnikbanerjee15

Yes, you are right. IsoQuant only normalizes by depth.

I think the common practice is that, unlike for short reads, counts obtained with long reads do not require gene/transcript length normalization, as one read typically represents one mRNA molecule.

Best Andrey