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Old 01-28-2013, 04:57 AM   #1
pbm13
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Default shuffleSequences.pl script in velvet

Hello,

I am trying to run velvet with RNAseq data from Illumina. While it does not say it in the velvet manual (that I saw at least), I have seen on other forums that you are supposed to interleave your fastq files to input into velveth for paired end reads and there is apparently a script associated with velvet called shuffleSequences.pl.
I would like to use this because I think that is part of some troubles I have been having getting velvet to run but I do not see this script in the velvet download tar file:
1) Do I need to use this for paired end sequences for velvet?
2) If yes, then where can I get this script?

Thank you for any help!
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Old 04-26-2013, 10:33 AM   #2
eni
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Default shuffleSequences.pl location

When you install velvet, it puts the shuffleSequences.pl in the contrib folder.
Copy the file to your local directory and you should be fine...

Last edited by eni; 04-26-2013 at 10:41 AM.
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Old 04-26-2013, 11:18 AM   #3
mastal
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Default shuffleSequences.pl script in velvet

what version of velvet are you using?

since version 1.2.06 you can use the flag -separate, and you don' t have to interleave the files.

see the velvet mailing list archives:

http://listserver.ebi.ac.uk/pipermai...ay/001705.html
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Old 05-19-2015, 06:47 AM   #4
kaps
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Quote:
Originally Posted by eni View Post
When you install velvet, it puts the shuffleSequences.pl in the contrib folder.
Copy the file to your local directory and you should be fine...
Hi, How do I locate the contrib folder for velvet?
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Old 05-19-2015, 06:49 AM   #5
GenoMax
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Quote:
Originally Posted by kaps View Post
Hi, How do I locate the contrib folder for velvet?
Look through the source code you downloaded.
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Old 05-19-2015, 06:59 AM   #6
mastal
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Default

velvet_1.2.10/contrib/shuffleSequences_fasta
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Old 05-19-2015, 07:36 AM   #7
kaps
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Quote:
Originally Posted by mastal View Post
velvet_1.2.10/contrib/shuffleSequences_fasta
Ok. I have copied shuffleSequences_fastq.pl to my folder but when I run shuffling as; shuffleSequences_fastq.pl lib4_align.end1.fq lib4_align.end2.fq lib4_all_ends.fq.
I get an error as;
-bash: shuffleSequences_fastq.pl: command not found

where is the problem?
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Old 05-19-2015, 08:05 AM   #8
kaps
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Quote:
Originally Posted by mastal View Post
what version of velvet are you using?

since version 1.2.06 you can use the flag -separate, and you don' t have to interleave the files.

see the velvet mailing list archives:

http://listserver.ebi.ac.uk/pipermai...ay/001705.html
Noted. this option is further supported here: http://thegenomefactory.blogspot.com...sequences.html.

I will not use shuffleSequences.pl!

Thanks
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