Mapping reads to 5 UTR, 3 UTR and CDS

Question

[student12]

Hello Everybody,

I am a beginner and was wondering how could I use my bam file to create plot showing the reads distribution in 5 UTR, CDS and 3 UTR region. Something similar to the plot attached. Thank you.

Ref: https://pubmed.ncbi.nlm.nih.gov/34437837/

[GenoMax]

Do you have access to a GTF annotation file with the UTR's and CDS? You can create a BED format file with those regions and then use a tool like mosdepth (LINK) to check read depth in those areas. Once that is done you can plot the data.

Code for RiboSeq analysis included in the paper you linked is made available here.

[student12]

Thank you for your help, will definitely look into it. Checked it on the github, but only found bar plots showing the percentage of genomic regions.