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I have performed RNA-seq analysis using HISAT2 & StringTie workflow suggested in: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Some of the transcripts/exons have decimal coverage values (eg., 1.1 or 2.59).

My question is: How can these tools report decimal coverage? If only half of the read overlaps exon will this exon have 0.5 coverage?

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I suspect this is average coverage across the transcript or exon.

Formula for average coverage:

coverage-formula

Where:

  • N: number of reads mapping/aligning to your transcript/exon
  • L: average read length
  • T: Transcript/exon length
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