After read mapping, count exons or genes? · Biostar

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After read mapping, count exons or genes?

I have mapped my RNA-seq reads (paired-end) onto the reference genome. Now I hope to measure the expression level by genes using featurecounts. Do I count the number of reads mapped to the whole 'gene' region, which includes introns? Or I should count reads mapped to all exons belonging to the same gene? Someone suggested using exons, may I know the reason behand this?

rna-seq featurecounts genome

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updated 6.2 years ago by ATpoint

• written 6.2 years ago by tianshenbio

1 answer

Exons because that is what the final spliced transcript is composed of. There is a reason that exon is the default setting in featureCounts.

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written 6.2 years ago by ATpoint

Ok now I understand, thank you.

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written 6.2 years ago by tianshenbio

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