We are all familiar with rseqc genebody coverage functions https://rseqc.sourceforge.net/#genebody-coverage-py. But I was wondering if there is an existing implementation of transcript level coverage with each of the features of transcript (like 5'UTR, CDS,exons, and 3' UTR) shown on the x-axis together.
I actually have transcriptome data for nanopore (from minimap2) which does not output chromosome names/locations instead it has transcript name and positions relative to transcript.
ENST00000575319.1 1 0
ENST00000575319.1 2 0
ENST00000575319.1 3 0
ENST00000575319.1 4 0
ENST00000575319.1 5 0
ENST00000575319.1 6 0
ENST00000575319.1 7 0
ENST00000575319.1 8 0
Here column1 is transcript id column2 is transcript position and column3 is read depth at that position. I would ideally like to plot this read depth and divide it by feature but show it on the same axis/facet.
I know RCAS (https://www.bioconductor.org/packages/release/bioc/vignettes/RCAS/inst/doc/RCAS.vignette.html) has something like that but it takes chromosome-level data but that's not what we have here. I was wondering if someone has experience with nanopore data and has tried to plot such a plot. Or there is an existing tool that does that?
I would appreciate any pointers in this regard.