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Old 10-18-2011, 09:51 AM   #1
Location: Farmington CT

Join Date: May 2011
Posts: 31
Default interpreting gene/transcript names from UCSC table browser human all_mrna

We are hoping to do a comparison of samples using tophat/cufflinks and a GTF file we got from the UCSC table browser (all human mRNAs).

Does anybody have any idea how we can convert the accession # / Codenames for these transcripts into something more meaningful (like: gene_name-exon_#). As it is we get the accession # for the transcript/exon but for a large number of transcripts this is not easy address and so it would be nice if we could use a script to convert them to something more immediately useful.
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Old 10-18-2011, 10:42 AM   #2
Location: USA

Join Date: Apr 2009
Posts: 36

using the biomaRt package in R makes this kind of thing really easy with ensembl:
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