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

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

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!

stringtie cufflinks ballgown deseq2
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updated by Ram Ram • written by Nina • Nina

1 answer

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

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written by Ram Ram

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