Hi Tracy, The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put the two together. Then set the datatype to fastq, if needed (click on the "pencil" icon for the full dataset to reach the "Edit Attributes" form to make the change). Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using "Filter and Sort -> Select" with the options "that: NOT Matching" and "the pattern: ^$". (the regular expression '^$' [no quotes] matches empty lines). I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us. Thanks for using Galaxy! Jen Galaxy team On 10/27/11 11:58 AM, Qingquan Liu wrote:
Hi Jennifer,
I have sequenced one sample on 2 lanes of GAII, and now I am trying to merge the 2 fastq files. How should I do it on Galaxy? Thank you very much!
Best,
Tracy
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Jennifer, just out of curiousity, is the command a linux cat? or does it actually parse the fastq sequences? asking as my service provider actually just split my PE files by lines (not no. of reads ) in fastq assuming that I can't merge them in galaxy, I am merging them properly then splitting them again (anyway i can map using concurrent processes and merged the bam later on Cheers Kevin On Fri, Oct 28, 2011 at 10:30 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Tracy,
The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put the two together. Then set the datatype to fastq, if needed (click on the "pencil" icon for the full dataset to reach the "Edit Attributes" form to make the change).
Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using "Filter and Sort -> Select" with the options "that: NOT Matching" and "the pattern: ^$". (the regular expression '^$' [no quotes] matches empty lines).
I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us.
Thanks for using Galaxy!
Jen Galaxy team
On 10/27/11 11:58 AM, Qingquan Liu wrote:
Hi Jennifer,
I have sequenced one sample on 2 lanes of GAII, and now I am trying to merge the 2 fastq files. How should I do it on Galaxy? Thank you very much!
Best,
Tracy
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/**Support<http://galaxyproject.org/wiki/Support> ______________________________**_____________________________ 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:
http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello Kevin, This particular function is like a "cat" - will work any text file. Assuming that you run the function in the same order the data was split, it should merge fine. Should you want to work with tools that manipulate FASTQ files specifically, a tool search of "FASTQ" will bring up most plus look under the tool group "NGS: QC and manipulation -> Generic FASTQ manipulation". And in case you didn't see this, data can be uploaded using FTP. Several compressed formats are support. Using a desktop client can the track progress of, restart, and confirm a load. http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP Best wishes for your project, Jen Galaxy team On 10/27/11 9:01 PM, Kevin Lam wrote:
Hi Jennifer, just out of curiousity, is the command a linux cat? or does it actually parse the fastq sequences? asking as my service provider actually just split my PE files by lines (not no. of reads ) in fastq
assuming that I can't merge them in galaxy, I am merging them properly then splitting them again (anyway i can map using concurrent processes and merged the bam later on
Cheers Kevin
On Fri, Oct 28, 2011 at 10:30 AM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hi Tracy,
The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put the two together. Then set the datatype to fastq, if needed (click on the "pencil" icon for the full dataset to reach the "Edit Attributes" form to make the change).
Be sure to watch out for an extra newline being added between the two files. You can test for/eliminate this using "Filter and Sort -> Select" with the options "that: NOT Matching" and "the pattern: ^$". (the regular expression '^$' [no quotes] matches empty lines).
I am sending to the galaxy-user mailing list for our internal tracking and for other users to learn from. Please send all questions directly to the list going forward, it is very helpful for us.
Thanks for using Galaxy!
Jen Galaxy team
On 10/27/11 11:58 AM, Qingquan Liu wrote: > Hi Jennifer, > > I have sequenced one sample on 2 lanes of GAII, and now I am trying to > merge the 2 fastq files. How should I do it on Galaxy? Thank you very much! > > Best, > > Tracy >
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/__Support <http://galaxyproject.org/wiki/Support> _____________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://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 <http://lists.bx.psu.edu/listinfo/galaxy-dev>
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
participants (2)
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Kevin Lam