retrieve genomic coordinate on mRNA

Question

[flower_des_iles]

Dear all, Is there an easy way to convert genomic coordinate to mRNA (transcript) coordinate (with no intronic region) ? I managed to convert genomic coordinate to gene coordinate (with intron) but i would like to find the coordinate on mRNA. Thanks,

[Istvan Albert]

What are you looking to obtain? As you point out a transcript is built from several different genomic coordinates, not just one.

Answer 1

[flower_des_iles]

I have genomic coordinate of iCLIP data. I want the coordinate of this proteine at the transcript level. I know that transcript are spliced and I want the coordinate on every transcript if the binding site doesn't occure in intron.

Answer 2

[Manvendra Singh]

It should be very simple

1. download the gtf file and install bedtools
2. convert it to bed using gtf2bed
3. grep -wi 'exon' bed_file_converted_from_gtf > exons.bed
4. intersectBed -a your_iCLIP_coordinates -b exons.bed > your_protein_binding_transcripts.bed

hth

Answer 3

[cmdcolin]

Tools like Ensembl VEP can do this, and will output things like cDNA position and CDS position (e.g. with or without counting the UTR)

The https://mutalyzer.nl/ tool also looks interesting

These may not be the most lightweight or purpose built, and only may work on certain organisms

I think the reason for not having such a purpose built tool is that it can be a complex task given the nature of things like overlapping genes or similar phenomenon, so VEP and other tools make best-attempt efforts to report all possible results

Answer 4

[Noushin N]

Transvar webserver can handle this task.

As you said, there will likely be multiple hits for each genomic positions.