Hello Assif, I am assuming that you are using the Table browser and the RefSeq Genes track and want output = sequence.
For this case, Downstream means the genomic sequence past the 3' region of the transcript alignment (past the 3' UTR). If you select Upstream sequence plus Downstream sequence and put it together into the same fasta record as output, then genomic sequence surrounding the gene would be in the output. A Blat alignment with this type of sequence would have two alignment blocks, span the gene bound, and have a single gap where the transcript aligned. Not what you want. Follow these steps to generate the correct 1200 bases using the Table browser 1) Start with the RefGene track and region = genomic 2) Select output as "Custom track" and "get output". 3) Choose upstream region 1000 bases and output in Table browser and submit 4) In the group pull-down menu, the top line will hold your custom track. Select this. 5) Select output as "Sequence". Name to download file (gzip recommended) and "get output". 6) Now set downstream region as 200 bases and submit. The zipped fasta file should download. Note: Downstream still means 3' from the input region, but since the custom track only contains the 1000 bases upstream per gene, Downstream will extract contiguous genomic sequence. The resulting sequence will be genomic 1000 bases upstream of the RefSeq's transcription start site (start of 5' UTR alignment) plus 200 bases downstream. Try with a single sample sequence first to verify that the steps are working correctly. Simply take the final sequence output, run a Blat, and view in Assembly browser to confirm. My test sequence was NM_000808 and the sequence output using this method is below. A quick Blat against human genomic using this sequence will show that it covers the region you describe (turn off all tracks except for the Blat result and RefGene to view clearly). Good luck and please let us know if you need more help, Jennifer Jackson UCSC Genome Bioinformatics Group >hg18_ct_tbrefGene_NM_000808_up_1000_chrX_151370488_r >range=chrX:151370288-151371487 5'pad=0 3'pad=200 strand=- repeatMasking=none TATTTCCATTACCATTCATTTGGTCACTGAGGATATTGAGGGCCAGATTG AAGAACTCGTTGAAAGCAACACAGCAATTTTCAGAGGCAGAACTCAAACT CAAGTTCCTTTATTTTATTTTTAGCCTAGGTCTTTTTCCACTCTATGCTG CATTGTTACTGTGCTTTGCCTAGGTTGCTTTTTTTCTTTTGACCCAATGG GAATATAGTTCTTTTATACTTTGAGTCAATAATTATCCTTCTCCCCACCT TAGTCCTTGTGCAACTCATGTATAGGCTCACACAATTACATACATCTATA TTCCCTTTGGAATTTTTGAAAAGAAAGCATTGTGGTTCTGCTGCTTGTCT GTCTTACCTACAGGGAAGCTAGAACTGATAGTTTTGAATTGGGTCTGCAC TTCTACTTGGTTGAGGGTGGGGGTGGAAGTTAGGTCAACAGGGGATCAAT GTGGCGGAACTCTTTCTTCTTAGTGGAGTATGAATGACAACCCCTTTGAT GTACATTTTTCTAGCTCATTATTGTCCCCAGAGATGGAATCTGAACAGAC AGGATTGTCAAACCTTTATTTGCAGCCTGGGTTAGAAGGCACGCCCATAA GGATATAAGGGAGACAGAGGGAAAAAGGAGGAAGCTCACTCTTCAGTCTC GGAGCAGCAAGTAAGCATCACACATCAGCTACAGTAACCCATACTTCCTT TATCCTCCTATTCGCTCATACCCTTTTGCTCTCTTTCTCTTCCCTTTGCT GCCTCTGCTCCTCCCTTTCTCTCTGGGCTTCCCTCTATTTCTCTGTTGGA TGCCTTAAGGAATAAAATACTACTTTAGTATTTCGTAAAACAACCACATC TAAAGCCTTGCAGTACTGTATTCAGAGCCCCAGCACAGCCGCGTGCTAAG CACCAGTGGTGAACCTAAAGCCAGCAAAGGGGGAGGGGAGAAGGGGAGGG GAGGAGGGGAGGGAGAAACTGACAGAGAGGGAGGGAGGCAGATTGAGAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGCGTGAGCGC GCGCAAGCTAGCGAGCAAACCAGAGAGACAGACCGAGAGAGGGACCAGGA GAGAGACCCAGAGAGAGAAGAAGAAGCCAGAAGCCGAGCTCTGTCAGGGC TCAACCTCCAACTTGTTTCAGTTCATTCATCCTTCTCTCCTTTCCGCTCA Assif Yitzhaky wrote: > Dear Supporter, > > In the Sequence Retrieval Region Options: > > What does it mean "Downstream by 200 bases"? downstream from the TSS? If not, > from what? > > I would like to download for each RefSeq, a sequence of 1200 bases; 1000 > upstream the TSS and 200 downstream from the TSS. I prefer not to download > the entire gene and truncate. > > As I remember, some time ago it was possible. How can I do that? > > Thank you, > > Assif. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
