GTF file from Stringtie to R Studio for either Ballgown or DESeq2
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5 weeks ago
Nina • 0

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 • 358 views
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5 weeks ago
Ram 44k

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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