StringTie FPKM output to DESeq2 input

Question

[Akash D]

How can StingTie GTF which contains FPKM values of the transcripts be transported to DESeq2 ? In there any step that has to be incorporated somewhere between StringTie and DESeq2 to make DESeq2 easily read the expression values?

Any help will be appreciated

Thnks Akash

[Akash D]

Will it be better to use TPM and not FPKM values from StringTie then? In that case will the tximport usage (To pass TPM values to DESeq2) still remain valid?

[Nitin Narwade]

TPM, RPKM, FPKM all are normalized read count and DESeq has its own normalization method. So it is not advisable to use normalized count to run DESeq, you should provide a raw read count. You can use HTSeq to calculate the raw read count and perform differential gene expression analysis using DESeq.

[Akash D]

Thank you so very much. Will try and surely get back

[mgranada3]

Does StringTie normalize the FPKM output?

Answer 1

[Nitin Narwade]

There is a way to import StringTie output in the R environment and you can use the matrix to perform DESeq differential gene expression analysis but It is not advisable to use FPKM as input for DESeq and EdgeR

Importing transcript abundance with tximport

DESeq2 robust fpkm error with tximport

[Akash D]

Thank you, Sir.