VelvetOptimiser sam format

pederworning · 06-23-2011, 03:42 AM

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

mht · 12-23-2012, 04:41 PM

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

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06-23-2011, 03:42 AM	#1
pederworning Junior Member Location: Copenhagen, Denmark Join Date: Feb 2011 Posts: 5	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

12-23-2012, 04:41 PM	#2
mht Member Location: California Join Date: May 2012 Posts: 23	Hi, I'm now trying to use velvetoptimiser on sam files too. Did u get any feedback on this issue?