14 May 2013
velvet, oases, transcriptome, and NuGENNext post Previous post
Aphaenogaster transcriptome assembly.
(Re)read the Oases paper and manual.
Installed newest version of velvet and oases.
As we will have reads up to 100bp, set MAXKMERLENGTH=66 for both velvet and oases as I somewhere recall seeing that max kmer should be about 2/3 length of reads. Will be getting 100bp reads.
Did some reading on best practices for software installation in linux so that programs will be available to all users. Cloned programs
git clone git://github.com/dzerbino/velvet.git into /opt/software. Ran
make and then symbolically linked
ln -s \opt\software\velvet\velveth into so that the programs are available to all users.
Useful tutorial for running velvet
Useful post about kmer
NuGEN Ovation 3’ DGE –> NuGEN Encore Rapid Library Prep.
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