Hi Tony,
Yes, that should work too. I have written up a BioPerl hack that indexes the reads and pulls out the pairs that is chugging away right now. If that does not work out somehow, I will give your idea a shot. Thanks!
Best, Surya
On Tue, Mar 29, 2011 at 4:20 PM, Barbet,Anthony F barbet@ufl.edu wrote:
Can you not do fastq join on the 2 files, fastq filter for the single (same max and min bases) full length combined size (and quality if you want), then fastq splitter?
Tony ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [ galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Surya Saha [ ss2489@cornell.edu] Sent: Tuesday, March 29, 2011 4:00 PM To: Anton Nekrutenko Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Combining the paired reads from Illumina run
Hi Anton,
Thank you for the tip. The sequence names do end in /1 and /2 but that can be fixed using Manipulate FASTQ tool, right?
-Surya
On Tue, Mar 29, 2011 at 3:46 PM, Anton Nekrutenko <anton@bx.psu.edu mailto:anton@bx.psu.edu> wrote:
You can try converting fastq to tabular (NGS: QC and Manipulation).
Jointing (Join, Subtract and Group) the two files on ids (provided they do not have /1 and /2). Splitting into two files with cut (Text manipulation), and going back into fastq with tabulat-to-fastq (NGS: QC and Manipulation). With 30 mil reads this will likely take some time though.
Thanks, anton
On Mar 29, 2011, at 11:38 AM, Surya Saha wrote:
These are Illumina reads
-S.
On Tue, Mar 29, 2011 at 11:37 AM, Anton Nekrutenko <anton@bx.psu.edu
mailto:anton@bx.psu.edu> wrote:
Are these illumina or solid reads?
Tx,
anton
On Mar 29, 2011, at 11:29 AM, Surya Saha wrote:
Hi,
I have two fastq files with the forward(/1) and reverse(/2) paired
reads. The reads are not in same order in either file, some pairs are absent/missing and the files are 8 GB each with abt 30 mill reads each.
I am trying to pull out all the paired reads for which both fwd and
rev exist. Can I use a combination of fastq tools in Galaxy to do this?
Thanks!
-Surya ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on
the list by
using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org