How can i get gene name instead of gene ID from prepDE.py after STRINGtie?

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6.3 years ago

k.kathirvel93 ▴ 310

Hi EveryOne,

I am trying STRINGtie for RNA-seq mRNA quantification after mapping with hisat2. STRINGtie can't produce gene raw counts, so i have used prepDE.py script to obtain gene counts. But, here i am getting only ensembl ID. I want gene name instead of ID. Any solution ? Thanks in advance.

RNA-Seq next-gen gene • 3.2k views

ADD COMMENT • link 3.4 years ago by k.kathirvel93 ▴ 310

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Can you add the command you ran along with a few lines from the input GTF files ?

ADD REPLY • link 6.3 years ago by lakhujanivijay 5.9k

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I am facing the same issue. Please help me in solving this issue.

ADD REPLY • link 6.2 years ago by arshad1292 ▴ 110

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Hi arshad1292,

I found the way by myself, First go to normal stringtie gene abundance file and reorder the ensemblID column in alphabet order with extent selection and copy gene ID column. Second go to PrepDE.py output file gene_Count_matrix.csv, and reorder the ensemblID column in alphabet order with extent selection and replace the geneID column by the copied geneID column from previous. This you can do in R also very easily. all the best

ADD REPLY • link 6.2 years ago by k.kathirvel93 ▴ 310

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Could you also, share how do we do that on R? I think I have gone way ahead of that PrepDE.py step!! Thank You!!