Question: RNA-SEQ count matrix: conversion of ensemble transcript ID to gene ID
gravatar for Duckula
2.6 years ago by
Duckula20 wrote:

Hello all, I would like to do DEG analysis on my count matrix using DESEQ2 package in R. My reads are in Ensembl Transcript ID and I know that I need to convert them to gene ID and sum up the reads belonging to the same gene before DEG, I know the package tximport for kalisto files but I have never done such directly from count matrix. Does anyone have some experience to share that how can I proceed?

Thanks a lot! p.s. the species is mmusculus (mouse)

id conversion rna-seq deseq2 R • 2.3k views
ADD COMMENTlink modified 2.6 years ago by Arup Ghosh2.7k • written 2.6 years ago by Duckula20
gravatar for Arup Ghosh
2.6 years ago by
Arup Ghosh2.7k
Arup Ghosh2.7k wrote:

The following is an example code for annotations using AnnotationDbi R package. Change res to the DESeq result object and the annotation file to the desired organism.

#Mouse annotations
res$symbol = mapIds(,
res$name =   mapIds(,
write.table(res,file='res_with_annotation.tsv', sep ="\t",quote = F)
ADD COMMENTlink written 2.6 years ago by Arup Ghosh2.7k

Thanks a lot! I will try it out to see the results !!

ADD REPLYlink written 2.6 years ago by Duckula20

Hi again! thanks a lot ! but this package only converts ensemble gene IDs to gene symbol but I have a ensemle transcript IDs and I also need to sum them up if they belong to the same gene. Do you have any other suggestions?

ADD REPLYlink written 2.6 years ago by Duckula20

Then a better idea will be to fetch them from reference GTF file.

ADD REPLYlink written 2.5 years ago by Arup Ghosh2.7k
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