Genomic coordinates for transcripts

Question

[win]

Hi all, i have transcript IDs such as

NM_001250.5, NM_000073.2

and many more. I wanted to know how could I get hg19 genomic coordinates for each one. I have tried this on UCSC genome browser and wanted to know if it can be automated.

any pointers in this direction could be most helpful.

thanks.

[vinayjrao]

If I understand your question, you can go to UCSC table browser, select hg19, and RefSeq genes under Track and RefGene under Table. Could you also explain about what process you wanted to automate?

Answer 1

[Sej Modha]

You can download the most recent annotation file from: http://www.ensembl.org/info/data/ftp/index.html, GTF/GFF3 file should contain coordinates for genes and transcripts.

Answer 2

[michael.ante]

You can use the UCSC table browser by selecting hg19 as assembly and "RefSeq genes" as track.

Then paste or upload your transcripts in the "identifiers (names/accessions):" field.

As "output format" you can choose either gtf or bed, and et voilá, you have your positions.