Mapping reads to 5 UTR, 3 UTR and CDS

0

Entering edit mode

2.7 years ago

student12 • 0

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. enter image description here

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

UTR mapping CDS • 992 views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 2.7 years ago by student12 • 0

0

Entering edit mode

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.

ADD REPLY • link 2.7 years ago by GenoMax 142k

0

Entering edit mode

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.

ADD REPLY • link 2.7 years ago by student12 • 0

Login before adding your answer.