Hello, If you have exon coordinates and want to find transcripts of characterized genes that overlap them(?), then you can use the table browser to extract fasta sequence.
The steps would be: 1) Upload the coordinates in one of the custom track formats 2) Identify the track you want to pull transcripts from (UCSC Genes, RefSeq Genes) 3) Perform an intersection starting with the gene track using your custom track as a filter 4) Output as fasta sequence The intersection process is described in detail in the Table browser help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html And here is Custom track help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Try this and let us know if you need specific help once you get started. If I have misinterpreted your question, please send more information to clarify. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Valeria Vasta" <[email protected]> wrote: > From: "Valeria Vasta" <[email protected]> > To: [email protected] > Sent: Wednesday, December 2, 2009 4:22:20 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] getting fasta starting with a list of chromosome coordinates > > Hello > > > > I have to align illumina reads to the targeted sequence that has been > captured for sequencing i.e a long list of exons coordinates. Can you > please let me know how can I obtain the fasta files to use as a > reference for the aignment? > > > > Thanks > > > > > > > > Valeria Vasta > > Assay Development Scientist | Biochemical and Molecular Genetics R&D > > Seattle Children's Research Institute > > 206-884-7674 OFFICE > > 206-987-7660 FAX > > [email protected] > > OFFICE 1900 9th Ave, Seattle, WA 98101 > > MAIL C9S-9 > > WWW seattlechildrens.org <http://seattlechildrens.org/> > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information protected by law. Any > unauthorized review, use, disclosure or distribution is prohibited. > If you are not the intended recipient, please contact the sender by > reply e-mail and destroy all copies of the original message. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
