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VelvetOptimiser sam format



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

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  • pederworning
    started a topic VelvetOptimiser sam format

    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.

    Peder Worning