Velvet usage

[caiosuz]

Hi everyone!

I'm trying to use velvet to work with unmapped_reads of a rna-seq experiment, to make a kind of quantification of the contaminants of my sample.

I was reading this quick guide about velvet usage http://www.embnet.org/sites/default/...d_Oases-QG.pdf and some doubts occurred me:

1st doubt - It's written that -exp_cov must be used only with genomic data, so, I can't use it my data, ok?
2nd doubt - If I mustn't use the -exp_cov, can I use the -cov_cutoff?
3rd doubt - How are the coverage values calculated? Is it a kind of percentage related to the size of each read?

Thank you all!

[Brian Bushnell]

Velvet is probably not the best assembler to use for assembling assorted junk in RNA-seq, which will probably have very high coverage variability. You might try Spades or Tadpole, both of which are much more tolerant of strange input, and don't need fixed coverage settings.