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Old 10-17-2013, 06:31 PM   #1
Andres_Gomez
Junior Member
 
Location: Urbana, IL

Join Date: Aug 2013
Posts: 8
Default Coverage peak values meta-velvetg

Hi

I have a metagenomic dataset composed by ~300 Million pair end reads (HiSeq) 150 bp read length and ~380 average fragment size.

I'm trying to run meta-velvet to assemble metagenomes. After choosing a kmer size of either 51 or 75 I see no difference between outputs from velvetg and meta-velvetg.

Furthermore, after running EstimateCovMulti.py, I end up with a -1 coverage peak value for both velvetg and meta-velvetg and the same very low N50 (~399). Strangely, that does not happen with all my samples.

Can anybody give me some clues as to what's going on here?

I'd really appreciate it

A
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