Hi Viki, I apologize for the delayed response. If I am understanding correctly, the table browser is capable of what you request.
In order to obtain the sequence from -500 bp to +100 bp relative to the TSS, set the table browser output to "sequence" as you output and click submit. Select "genome" and on the next page, in the Sequence Retrieval Region Options section, make the following selections (unselect anything else that may have been selected by default in this section): * Promoter/Upstream by _500_ bases * One FASTA record per region (exon, intron, etc.) with _0_ extra bases upstream (5') and _100_ extra downstream (3') Restricting your query to only the canonical genes is a two step process. Follow the first set of directions, "Getting a list of canonical genes," on this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2010-September/023431.html Then: 1. Return to the Table Browser and select "knownGene" from the table pull down menu. 2. Upload our list of canonical genes: click "upload list" next to identifiers. Select your file and click "submit". 3. Continue with the output selections I described above. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Viki S wrote, On 03/25/11 12:59: > Hi, > I want to download promoter sequences of hg19 assembly with -500bp to +100 bp > relative to the TSS. Moreover this sequences should be one per known Entrez > ID/gene symbol. > In a table browser I was able to select upstream sequences, but could not > find option how to select entire sequence from -500 bp to +100 bp relative to > the TSS. > And how to filter out redundant sequences for each gene and allowing only one > sequences per Entrez gene (by criteria for example, canonical transcript ) > > Thanks > V > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
