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Old 09-19-2018, 05:02 PM   #1
Junior Member
Location: Israel

Join Date: May 2011
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Default featureCounts - does it normalize by gene length?

I'm starting to analyze RNA seq data, and I was hoping you can please help me clear something up

I am using FASTQ groomer, then TopHat2 to align, and then featureCounts, to get a number of reads per gene.

Is the numbers of reads per gene (output) of featureCounts normalized to the gene length?
If not, how can I do that? I want to end up with number of reads per gene, regardless of isoforms etc.

bzguy is offline   Reply With Quote
Old 09-20-2018, 04:22 AM   #2
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featureCounts is going to count reads per feature ("-t exon") that you specify and then will summarize the counts per gene ("-g gene_id"). It is going to report raw read counts and does not normalize the data.
GenoMax is offline   Reply With Quote

featurecounts, normalization

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