Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized
Hi , Looks like the tool Divide FASTQ file into paired and unpaired reads is not recognizing my paired-end naming suffix @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA Is there a patch for this or another tool/way I can divide this fastq file? Thanks in advance, Liisa
On Fri, Dec 9, 2011 at 4:49 PM, Liisa Koski <liisa.koski@dnalandmarks.ca> wrote:
Hi , Looks like the tool Divide FASTQ file into paired and unpaired reads is not recognizing my paired-end naming suffix
@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
Is there a patch for this or another tool/way I can divide this fastq file?
Thanks in advance, Liisa
That's a new Illumina FASTQ file isn't it, where they went and changed the read naming? That annoyed quite a few people... Presumably you're talking about my tool of that name on the Galaxy Tool Shed? I can take a look at this now if you agree to test it ;) Peter
Thanks Peter! That would be great! Let me know when you want me to test it :) Cheers, Liisa Liisa Koski Bioinformatics Programmer Phone: 450-358-2621 x104, E-Mail: liisa.koski@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at support@dnalandmarks.ca.----Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à support@dnalandmarks.ca. From: Peter Cock <p.j.a.cock@googlemail.com> To: Liisa Koski <liisa.koski@dnalandmarks.ca> Cc: galaxy-dev <galaxy-dev@bx.psu.edu> Date: 2011-12-09 11:55 Subject: Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized On Fri, Dec 9, 2011 at 4:49 PM, Liisa Koski <liisa.koski@dnalandmarks.ca> wrote:
Hi , Looks like the tool Divide FASTQ file into paired and unpaired reads is not recognizing my paired-end naming suffix
@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
Is there a patch for this or another tool/way I can divide this fastq file?
Thanks in advance, Liisa
That's a new Illumina FASTQ file isn't it, where they went and changed the read naming? That annoyed quite a few people... Presumably you're talking about my tool of that name on the Galaxy Tool Shed? I can take a look at this now if you agree to test it ;) Peter
On Fri, Dec 9, 2011 at 5:05 PM, Liisa Koski <liisa.koski@dnalandmarks.ca> wrote:
Thanks Peter! That would be great! Let me know when you want me to test it :) Cheers, Liisa
The revised code is here on bitbucket (on the branch "tools"), you'll need fastq_paired_unpaired.py and fastq_paired_unpaired.xml v0.0.5: https://bitbucket.org/peterjc/galaxy-central/src/7611d5d306bb/tools/fastq I'll put in on the Tool Shed next week if you're happy with the update. I've only had time to do a very quick test tonight. Regards, Peter
On Friday, December 9, 2011, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Dec 9, 2011 at 5:05 PM, Liisa Koski <liisa.koski@dnalandmarks.ca> wrote:
Thanks Peter! That would be great! Let me know when you want me to test
it :)
Cheers, Liisa
The revised code is here on bitbucket (on the branch "tools"), you'll need fastq_paired_unpaired.py and fastq_paired_unpaired.xml v0.0.5:
Try this (looks like I had the wrong link on Friday), sorry: https://bitbucket.org/peterjc/galaxy-central/src/a25f7920a1e5/tools/fastq Peter
Hi Peter, Thanks! The fix worked with the new Illumina format. Your help is much appreciated :) Cheers, Liisa Liisa Koski Bioinformatics Programmer From: Peter Cock <p.j.a.cock@googlemail.com> To: Liisa Koski <liisa.koski@dnalandmarks.ca> Cc: galaxy-dev <galaxy-dev@bx.psu.edu> Date: 2011-12-12 03:47 Subject: Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized On Friday, December 9, 2011, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Dec 9, 2011 at 5:05 PM, Liisa Koski <liisa.koski@dnalandmarks.ca wrote:
Thanks Peter! That would be great! Let me know when you want me to test
it :)
Cheers, Liisa
The revised code is here on bitbucket (on the branch "tools"), you'll need fastq_paired_unpaired.py and fastq_paired_unpaired.xml v0.0.5:
Try this (looks like I had the wrong link on Friday), sorry: https://bitbucket.org/peterjc/galaxy-central/src/a25f7920a1e5/tools/fastq Peter
participants (2)
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Liisa Koski -
Peter Cock