Also, if you have small number of regions that you want, just one time, like a list of a few thousand regions, you can simply make a custom track of it or paste it into the Table browser (hgTables), and choose sequence output.
By the way, we call (chrom, start, end) the BED3 format because it only uses 3 of the full 12 columns. -Galt On Fri, 14 Nov 2008, Galt Barber wrote: > > Seems like you'd get much faster results by simply > bulk-downloading the fasta files one time, > and then use something faFrags to grab a region. > > Also, you could make a .2bit file and twoBitToFa > options to select any subset region from the 2bit file. > > -Galt > > > On Fri, 14 Nov 2008, Gupta, Ashutosh (NIH/NCI) [F] wrote: > >> Hi, >> >> I want to be able to download genome sequences (without repeat masking, >> all upper case) for a given chrNum with start & end coordinates. >> >> >> >> Here is how it is done on the browser: chrX:151,073,054-151,383,976 with >> (0,0) flanking sequences upstream & downstream. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=115827007&o=151073053&g=getDna&; >> i=mixed&c=chrX&l=151073053&r=151383976&db=hg18&hgsid=115827007 >> >> >> >> Is there a way to stitch together a url so that this data can be >> generated (as if one was to press the getDNA button) or by the following >> link: >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=115827007&g=htcGetDna2&table=&i >> =mixed&o=151073053&l=151073053&r=151383976&getDnaPos=chrX%3A151%2C073%2C >> 054-151%2C383%2C976&db=hg18&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.paddi >> ng3=0&hgSeq.casing=upper&boolshad.hgSeq.maskRepeats=1&hgSeq.repMasking=l >> ower&boolshad.hgSeq.revComp=1&submit=get+DNA >> >> >> >> The FAQs page suggests not to use the hgsid variable, and I am not sure >> how to query without that. >> >> >> >> My question is pretty much the same as answered on the following page: >> >> http://www.soe.ucsc.edu/pipermail/genome/2008-August/017039.html >> >> , the only thing different is that I am not using a web browser. >> >> So creating or setting a session would not be helpful. >> >> >> My program accepts a url & reads the content of the given url in html or >> txt format. No browser is involved. >> >> >> >> All the necessary information has to be given in a single (or multiple) >> link(s) / string(s), based on parameters defined in the example above: >>> hg18_dna range=chrX:151073054-151383976 5'pad=0 3'pad=0 strand=+ >> repeatMasking=none >> >> >> >> Any help would be much appreciated. >> >> Thanks, >> >> Ashutosh. >> >> >> >> PS: Is there a way to get the whole desired sequence in one line? >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
