Hi Steve, I did try sra toolkit. In my case the difference between files is around 100mb.
I got fastq files by instructions mentioned at the following website ... http://seqanswers.com/forums/archive/index.php/t-8220.html Some issues I had with sra toolkit(I know this not the right place to discuss this still ...): FIrst I tried fastq-dump (a blank output file) and then illumina-dump which gave me a set of 1. *.qcal.txt( which contains sequences like "hhhhhhhhhhhehhhhhThhLhhL")and 2. *.seq.txt (which contains info like "1 1 875 885 TACATGGGGAAAATATGCAAAATA") I have yet to figure out how to convert this into fastq. Kirti On Fri, Mar 4, 2011 at 9:47 PM, Steve Lianoglou < [email protected]> wrote: > Hi, > > On Fri, Mar 4, 2011 at 2:34 PM, kirti prakash > <[email protected]> wrote: > > Hi Sean and Martin, > > > > Thanks a lot for the clarification. > > > > Do you some other function now that converts SRA to fastq format ? > > You can do it via the sra toolkit. Some info and download link here: > > http://www.ncbi.nlm.nih.gov/books/NBK47540/ > > > I wonder how much space NCBI saves by deleting fastq files and what is > extra > > advantage of having of SRA files. > > Run the (I believe) fastq-dump tool to convert to FASTQ and see for > yourself ;-) > > It's weird -- I have a set of *.fastq.gz files for a set of *.sra > files, and the corresponding *.fastq.gz files seem to actually be > smaller! > > Maybe it's just me, though ... > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
