Hi Rocky, Please read below:
UCSC Genome Browser Dear Mr/Ms, I would like to retrieve genomic coordinates with their miRNA predicted target sites from PITA tool using UCSC genome browser. I have tried on this link [ http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&hgt.customText=http://genie.weizmann.ac.il/pubs/mir07/ucsc/PITA_sites_hg18_0_0_TOP.bed.gz ] but could get the right answer. Could you please support me by sending the ftp site. I would be glad for your kindness. Response: The reason this custom track doesn't work is because the data used in this url (http://genie.weizmann.ac.il/pubs/mir07/ucsc/PITA_sites_hg18_0_0_TOP.bed.gz) is broken. You will need to contact the lab using this url: http://genie.weizmann.ac.il/index.html. ------------------------------------------------------------------------------------------------------------------------------------------------------------------- UCSC Genome Browser Group Dear Mr/Ms, I am attaching here a text file consisting of miRNAs predicted targets sites from UCSC genome browser. I would like to clarify is this file contains the true information for genomic coordinates for hg18 predicted PITA. I would be glad for your support. Response: Our mailing list software does not accept attachments. You can use our table browser to download the coordinates of the miRNAs you are interested in. You will have write a script to compare your data with UCSC data. To use the table browser to download the coordinates for the miRNAs. To use the table browser, click on "Tables" from the blue navigation bar (http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18) Set the clade, genome, and assembly. Then you will need to set the following: group: Gene and Gene prediction tracks track: UCSC Genes table: knownGene region: genome identifiers (names/accessions): click on "paste list" and paste in the gene symbol following the instructions. output format: selected fields from primary and related tables output file: fileName (name that you would like the file to be saved to) click "get output" select the fields you want displayed. click "get output" If you have further questions, please email: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
