hg19 transcript mapping or exon overlap
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7.1 years ago
bioguy24 ▴ 230

Is there a tool or script that can map or identify what exon the current version of an hg19 transcript overlaps with? I guess like UCSC genome browser but for just uses the coordinates without visualizing them. Thank you :)

For example.

 Transcript        Exon
 NM_001127222.1     10
NGS • 1.7k views
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I'm not sure, but do exon numbers make sense in the context of alternative splicing? There is no unambiguous way to number exons if some are optional.

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Do you mean you want to identify all exons of a transcript? If so you can use ucsc table browser (go to ucsc website -> tools -> table browser -> select clade: mammal; genome: human; assembly: hg19; group: genes and gene predictions; leave track and table as default -> either download genome-wide info or upload identifier, in your case NM_001127222 -> hit get output -> exon start and end positions are displayed as one of the default fields)

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Thank you all for your help :)

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WouterDeCoster .....i must talk to yuo...my email: pjalali46@yahoo.com.

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