Question: Using featurecounts for EdgeR input?
gravatar for nikelle.petrillo
2.9 years ago by
Providence College, Providence, RI
nikelle.petrillo90 wrote:


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

rna-seq edger rsubread de • 2.6k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 2.9 years ago by nikelle.petrillo90

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

ADD REPLYlink written 2.9 years ago by geek_y9.1k


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

ADD REPLYlink written 2.9 years ago by nikelle.petrillo90
gravatar for eldronzhou
2.9 years ago by
eldronzhou350 wrote:


You may find the following link helpful:

ADD COMMENTlink written 2.9 years ago by eldronzhou350
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1954 users visited in the last hour