I tested the get dna link with wget and it worked. wget -O dna.fa 'http://genome.ucsc.edu/cgi-bin/hgc?hgsid=189316231&g=htcGetDna2&table=&i=mixed&o=0&l=0&r=120614378&getDnaPos=chr13%3A1-120%2C614%2C378&db=mm8&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA'
2011-03-16 09:58:21 (61.0 MB/s) - `dna.fa' saved [123026758] ls -l dna.fa -rw-rw-r-- 1 galt protein 123026758 Mar 16 09:58 dna.fa It might be a problem with your browser. One should use hgdownload or hgTables for big sequences like whole chromosomes. -Galt On 03/16/11 08:20, Dr. Bhushan Bonde wrote: > Hi, > I am getting a very strange results when I compare the sequence of chr13 > (mouse mm8/NCBI36 release Feb2006) obtained as ftp as a > chr13.fa.gz(retrived from link > http://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/chr13.fa.gz ) > (call this a seqChr13_A.fa) and the DNA sequence of same chr13 obtained via > link > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=189316231&o=0&g=getDna&i=mixed&c=chr13&l=0&r=120614378&db=mm8&hgsid=189316231( > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=189316231&g=htcGetDna2&table=&i=mixed&o=0&l=0&r=120614378&getDnaPos=chr13%3A1-120%2C614%2C378&db=mm8&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA<[email protected]>) > (call this a seqChr13_B.fa ) > > What is strange is the FTP obtained Chr13 seq (seqChr13_A.fa) has 12614378 > bases which is correct as per the statistics of > http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=189336755&chromInfoPage= > However, when I check the same chr sequence obtained via browser > (seqChr13_B.fa ), it shows that the chr has only 54821374 bases. > So what happened to almost ~65MB sequences? Is this a known bug? Or Is this > something to do with internet browser not capable of loading 120MB file and > only loading the 54MB file in the browser? But then when I check the end of > the two files, the last 50 line sequence match correctly, means the end of > file was downloaded correctly via broswer. (Not to mentioned, I checked > various browsers on winodws/linux (both 32 and 64 bit) with Internet > explorer/firefox/google chrome and I get the same file back as > (seqChr13_B.fa ) . > > Thanks in advance, > > wishes, > > Dr. Bhushan Bonde > > Computational Biology, > > Medicines Discovery and Development, > > GlaxoSmithKline R&D, UK. > > > > > <[email protected]> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
