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Old 06-03-2016, 07:23 AM   #1
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 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
Old 06-03-2016, 10:16 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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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.
Brian Bushnell is offline   Reply With Quote

unmapped reads, velvet

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