DEGS analysis with DESeq2?
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.
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mathavanbioinfo
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Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
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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
Can you show us your
StringTiecommand?