Good Afternoon Duke: I believe you have the kent source utilities. In that case, you can run the conversion:
wget -O /dev/stdout \ "ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/all_mrna.txt.gz"; \ | zcat | cut -f 2- | pslToBed stdin stdout | bedToGenePred stdin all_mrna.gp with the result in the file all_mrna.gp --Hiram Duke wrote: > Hi Hiram, > > I am sorry for not being clear about my questions. The refFlat format is > what called gene prediction format: > > http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat > > http://genome.ucsc.edu/FAQ/FAQformat.html#format9 > > Thanks, > > D. > > On 12/27/10 12:09 PM, Hiram Clawson wrote: >> Good Morning Duke: >> >> Can you describe refFlat format ? I'm not familiar with that. >> >> The MySQL text dump: >> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/all_mrna.txt.gz >> >> is PSL format which is what "All fields" is from the table browser. >> >> --Hiram >> >> ----- Original Message ----- >> From: "Duke"<[email protected]> >> To: [email protected] >> Sent: Monday, December 27, 2010 7:56:00 AM >> Subject: [Genome] mRNA in genePred (refFlat) format >> >> Hi all, >> >> Anybody knows how I can download mouse mRNA track in refFlat format? The >> Table Browser can give me BED, GTF or All fields (which I dont really >> know what type of format it is), but not refFlat format. >> >> Thanks in advance, >> >> D. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
