Question: retrieve genomic coordinate on mRNA
2
gravatar for flower_des_iles
3.7 years ago by
flower_des_iles20 wrote:

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,

ADD COMMENTlink modified 3.7 years ago by Noushin N590 • written 3.7 years ago by flower_des_iles20
1

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

ADD REPLYlink written 3.7 years ago by Istvan Albert ♦♦ 86k
0
gravatar for flower_des_iles
3.7 years ago by
flower_des_iles20 wrote:

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.

ADD COMMENTlink written 3.7 years ago by flower_des_iles20
0
gravatar for Manvendra Singh
3.7 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

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

ADD COMMENTlink written 3.7 years ago by Manvendra Singh2.1k
0
gravatar for cmdcolin
3.7 years ago by
cmdcolin1.5k
United States
cmdcolin1.5k wrote:

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

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by cmdcolin1.5k
0
gravatar for Noushin N
3.7 years ago by
Noushin N590
Baltimore, MD
Noushin N590 wrote:

Transvar webserver can handle this task.

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

ADD COMMENTlink written 3.7 years ago by Noushin N590
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