Thread: Velvet usage
View Single Post
Old 06-03-2016, 07:23 AM   #1
caiosuz
Member
 
Location: Brazil_Bahia_Ilheus

Join Date: Dec 2015
Posts: 12
Default Velvet usage

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!
caiosuz is offline   Reply With Quote