Plot normalized coverage across genes/transcripts in single cell rna seq data

Question

[kevin.stachelek]

I'd like to generate a plot similar to the included image. What is the name of such a plot and does there exist a simple tool to generate, preferably compatible with multiqc and/or R/bioconductor?

Answer 1

[Kristoffer Vitting-Seerup]

Maybe CoverageView? Looks like it was made for other experiment types but since it uses bam files as input it might work. Else Bioconductors bamsignals have a bamCoverage() function

Else I know RSeQC have a gene-coverage tool which you can find here.

Just be aware that generally in single cell data (especially for 5' end data such as 10X) you have way to few reads per gene to look at coverage. Most genes have very few reads so how much sense it makes to calculate this I'm note sure.

[kevin.stachelek]

thanks. I'm working with Smart-seq data so I hope I have enough reads to make an intelligible plot.