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