14 May 2013

velvet, oases, transcriptome, and NuGEN

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Tuesday notes

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

Gene expression

NuGEN Ovation 3’ DGE –> NuGEN Encore Rapid Library Prep.

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