How can HISAT2/StringTie report decimal coverage values

Question

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?

Answer 1

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

Formula for average coverage:

Where:

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