DEGS analysis with DESeq2?

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4.3 years ago

mathavanbioinfo ▴ 90

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.

DESeq2 DEGs • 991 views

ADD COMMENT • link updated 4.1 years ago by Biostar 20 • written 4.3 years ago by mathavanbioinfo ▴ 90

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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

ADD REPLY • link 4.3 years ago by ATpoint 82k

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Can you show us your StringTie command?

ADD REPLY • link 4.1 years ago by MatthewP ★ 1.4k

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