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Using featurecounts for EdgeR input?

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

edger rsubread de rna-seq
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updated by Biostar Biostar • written by nikelle.petrillo nikelle.petrillo

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

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written by GouthamAtla GouthamAtla

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?

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written by nikelle.petrillo nikelle.petrillo

1 answer

Hi,

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

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written by GZ1995 GZ1995

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