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Old 10-15-2018, 07:42 AM   #1
lre1234
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Location: US

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Default converting postions in a gene to genomic coordinates

Hi all,
I'm interested in a way to convert the positions in a gene to the genomic coordinates. So for example, if I have Gene X, and position 200-400 of the mRNA. I would like to be able to get these positions in the mRNA to the genomic positions. It is possible that they would also span an intron-exon boundary which would at a 2nd level of confusion...

Thanks, for any help or advice
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Old 10-25-2018, 01:44 AM   #2
vivek_
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The easiest way would be to align the sequence using BLAT: https://genome.ucsc.edu/cgi-bin/hgBlat?command=start

If its a handful of bases you can use mutalyzer's position converter: https://mutalyzer.nl/position-converter
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