intro-to-rnaseq-with-galaxy

Gene Quantification

Counting reads for each gene

Our next step is to quantify the spliced reads that aligned to each gene in our GTF file For two non-overlapping, multiple-exon genes, our alignment may look like this:

The tool featureCounts is part of the subRead package.

Source

The result is a gene count matrix:

Running featureCounts

Question 8: Locate the "featureCounts:Assignment" plot, which shows whether reads were assigned to genes (features) or whether they failed to be assigned. What is the main reason for reads not being "Assigned"?

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