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Old 06-23-2011, 04:42 AM   #1
pederworning
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Location: Copenhagen, Denmark

Join Date: Feb 2011
Posts: 4
Default VelvetOptimiser sam format

Dear Bioinformatic forum,

I am using VelvetOptimiser to see which parameters to use for Velvet denovo assembly, but I cannot get it to read sam files. It can read fasta and fastq but not sam.
I am using Ubuntu 10.04 LTS installation and I have Velvet version 1.0.18 and VelvetOptimiser.pl version 2.2.0 My velveth can read the sam files!

When I do the following command I get the error message below:
> VelvetOptimiser.pl -s 15 -e 31 -f '-shortPaired -sam s_7_001.sam' -t 4 -g 3.0
MSG: The sequence does not appear to be FASTA format (lacks a descriptor line '>')

I have tried to shuffle the -shotPaired and -sam and if I type -fastq instead of -sam I get a different error message:
MSG: Missing sequence and/or quality data; line: 23774387
So it can read fastq but not sam.

Have anyone tried to read sam files with VelvetOptimiser and do you have any suggestions of what to do.

Thanks
Peder Worning
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Old 12-23-2012, 05:41 PM   #2
mht
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Location: California

Join Date: May 2012
Posts: 23
Default

Hi, I'm now trying to use velvetoptimiser on sam files too. Did u get any feedback on this issue?
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