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!
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Surya Saha