Question

Gene Start Stop

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12.6 years ago

bioinformatics123 ▴ 10

Hi! I am trying to extract start and stop positions for a gene list. Can someone suggests and files for homo sapiens that can be downloaded from which I can parse the info using perl? I know UCSC has files like knowngene and refgene but I am not sure about the formatting in those txt files. Any suggestions?

gene • 3.5k views

ADD COMMENT • link updated 12.6 years ago by seidel 11k • written 12.6 years ago by bioinformatics123 ▴ 10

score 2 · Answer 1 · 2012-04-16

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12.6 years ago

Istvan Albert 101k

Click the button called "describe table schema" and it will tell you what is in each column.

ADD COMMENT • link 12.6 years ago by Istvan Albert 101k

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May it would be easier for you to use the "Table Browser" and download the annotations as e.g. BED file. You can find an explanation of this format here:

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

ADD REPLY • link 12.6 years ago by Pascal ▴ 250

score 2 · Answer 2 · 2012-04-16

You might also try ensembl biomart. Given that you already have a gene list, ensembl has a web front-end you could use to extract the information you need, and you likely wouldn't have to use perl to parse out the results. You can select the fields you would like returned in a text file (i.e. start, stop).