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> 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> 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 ___________________________________________________________
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>> Anton Nekrutenko
>> http://nekrut.bx.psu.edu
>> http://usegalaxy.org
>>
>>
>>
>
>
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
>
>