Using featurecounts for EdgeR input?

Question

[nikelle.petrillo]

Hello,

I have paired end reads and I am performing de novo RNA seq. I used tophat to align my reads to a reference transcript I assembled in Trinity. Now, I would like to perform differential expression analyses in EdgeR. My understanding is that I can not simply input the accepted_hits.bam output file from tophat and that I need to use a program to give me a matrix of raw counts? I have decided to use FeautreCounts from the Rsubread package to produce these raw counts. However, I am new to R and this learning curve is a bit steep. Does anyone know how I should go about using FeatureCounts? I have read over the manual, there seems to be many arguments that can be used, which are necessary for RNA seq data?

Any help would be appreciated! Thanks, Nikelle

[GouthamAtla]

Do you have the coordinates for your genes/transcripts ? What kind of annotations you have ?

[nikelle.petrillo]

Hello,

Thank you for your reply. I'm not sure what you mean by coordinates/annotations? Do you know how i would find/generate these?

Answer 1

[GZ1995]

Hi,

You may find the following link helpful: http://genomicsclass.github.io/book/pages/rnaseq_gene_level.html