Question: DEGS analysis with DESeq2?
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gravatar for mathavanbioinfo
9 months ago by
India
mathavanbioinfo50 wrote:

Hello all, I am working in DEG analysis using DESeq2, I followed the protocol given in StringTie, the results file has very few genes ( mapped with AnnotationDbi,org.Hs.eg.db), and the genes start with MSTRG abundantly present. Is there any way to map MSTRG id gene ids or how to deal with that those ids.

degs deseq2 • 255 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 9 months ago by mathavanbioinfo50

Unless you really need stringtie in order to assemble a transcriptome just save yourself the trouble with this tool and use anything else. This workflow gives a much more simplistic while not at all less accurate suggestion on how to perform DGE from scratch:

https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

ADD REPLYlink written 9 months ago by ATpoint41k

Can you show us your StringTie command?

ADD REPLYlink written 8 months ago by MatthewP800
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