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)
Thanks a lot! I will try it out to see the results !!
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?
Then a better idea will be to fetch them from reference GTF file.