Transcript feature coverage with coverage of each feature shown like e.g. UTR's CDS, exons etc

Question

[Saad Khan]

Hi,

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.

Thank you!

Answer 1

[Hiba]

it might help :

https://github.com/HibaLaghrissi/Article_2023/blob/main/code/iCLIP_synaptosome/metaTranscript.ipynb

Answer 2

[Huiyang]

If I understand correctly, you want to calculate the coverage for each of the features of transcript. Then you can try PanDepth, which can calculate the coverage of exons/CDS based on gtf/gff files. Other types of features can be calculated using bed files.