Question: How To Get A List Of Coding Exons In Which Each Exon Is Represented Once.
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gravatar for Rehman, Atteeq (NIH/NIDCD) [F]
9.2 years ago by
Hey everyone, I am a new galaxy user. I am trying to upload coding exons of specific region from ucsc genome browser but I end up with loading coding exons of all splice variants/isoforms. As a result some exons are repeated many times (depending upon how many isoforms the crossponding gene has) which I don't want. Can somebody help me how can I have a list of coding exons in which each exon is represented only once irrespective of how many splice variants/isoforms the gene has? Thanks a lot [cid:image001.jpg@01CA41C8.B3A28E40] Atteeq Ur Rehman Visiting Fellow National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Room 2A-19, 5 Research court, Rockville, MD, USA, 20850. Lab Ph. No. 301-402-9059
galaxy • 1.5k views
ADD COMMENT • link • modified 9.2 years ago by Anton Nekrutenko ♦ 1.7k • written 9.2 years ago by Rehman, Atteeq (NIH/NIDCD) [F] • 20
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gravatar for Anton Nekrutenko
9.2 years ago by
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Rehman: Here is one way of dealing with this: 1. Upload genes from UCSC in bed format. 2. Use "Operate on Genomic Intervals --> Cluster" with "Return Type" option set to "Find largest interval in each cluster" (see attached image). This will select longest transcript for each gene. 3. Use "Extract Features --> Gene BED To Exon/Intron/Codon BED expander" to convert gene coordinates to exon coordinates. Let me know if you run into any trouble with this. Thanks for using Galaxy! anton galaxy team
ADD COMMENT • link written 9.2 years ago by Anton Nekrutenko ♦ 1.7k
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