Question: Using featurecounts for EdgeR input?
3
gravatar for nikelle.petrillo
2.9 years ago by
Providence College, Providence, RI
nikelle.petrillo90 wrote:

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

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

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?

ADD REPLYlink written 2.9 years ago by nikelle.petrillo90
1
gravatar for eldronzhou
2.9 years ago by
eldronzhou350
eldronzhou350 wrote:

Hi,

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

ADD COMMENTlink written 2.9 years ago by eldronzhou350
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