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> 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.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:
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