One additional clarification for this step in my prior email: 4) Configure output format to be complete table or only selected fields
The more direct way to extract only the 3' UTR coordinates is to set output format = BED. Then, after you name the file and click on "get output", a configuration page will come up. Select "3' UTR Exons" and submit. The coordinate rules still apply and BED file format is explained here: http://genome.ucsc.edu/FAQ/FAQformat#format1 If you have any questions, please let us know, Jennifer Jackson UCSC Genome Bioinformatics Group Anna Kosubek wrote: > Hello, > > is there a fast way to get the scaffold-number (and strand) that describes > the position of the stop-codon / start of the 3´UTR of a X. tropicalis > gene by using a RefSeq Transcript ID e.g. NM_001078970? > I need the scaffold-numbers for 3´UTR of about 2000 tropicalis genes, in > order to analyse micro array data (Affimetrix) for motifs in the 3´UTR, so > is there also a possibility to enter a list of RefSeq Transcript IDs and > receive a list of the according scaffold-position? > > Thanks a lot > > Ania > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
