Hello - sorry for the problem. I've looked into this a bit. It appears that after gunzipping them, they need to be bunzip2'd as well. This is a mistake that we'll try and fix, but in the meantime that is the workaround.
Venkat - can you take point in fixing this? On Dec 2, 2011, at 7:48 AM, Albert Vilella wrote: > Hi, > > I am looking at the fastq.gz files for the mouse ENCODE data at the > UCSC DCC website, and it looks like > all datasets coming from Caltech are zipped with some format other > than gzip. Can you tell me which one? > > For example, for any of the files *not* from Caltech, I can do gunzip: > > avilella@magneto:~/00x$ wget -qO- > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneEsb4InputME0C57bl6StdRawDataRep2.fastq.gz > | gunzip -c | head -n 4@SOLEXA2_0001:2:1:0:9#0/1 > NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN > +SOLEXA2_0001:2:1:0:9#0/1 > BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > > But for the ones from Caltech, I just get encoded gibberish back: > wget -qO- > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechHist/wgEncodeCaltechHistC2c12InputFCntrl50bE2p60hPcr1xRawDataRep1.fastq.gz > | gunzip -c | head -n 4 > > or > > wget -qO- > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12InputFCntrl36bPcr1xRawDataRep1.fastq.gz > | gunzip -c | head -n 4 > > Thanks in advance, > > Cheers, > > Albert. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
