shuffleSequences.pl script in velvet

[pbm13]

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!

[eni]

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...

[mastal]

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/pipermail/velvet-users/2012-May/001705.html

[kaps]

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?

[GenoMax]

Hi, How do I locate the contrib folder for velvet?

Look through the source code you downloaded.

[mastal]

velvet_1.2.10/contrib/shuffleSequences_fasta

[kaps]

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?

[kaps]

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