GTF file from Stringtie to R Studio for either Ballgown or DESeq2

Question

[Nina]

I used the stringtie -e -B command and received a file like the one attached to this post

When using it in R, I received an output saying that I needed a .ctab file. I tried using the cufflinks environment with the tablemaker command but it said that there was no such command.

I really appreciate any advice!

Answer 1

[Ram]

See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#StringTie