Velvet Can'T Handle K-Mers As Long As ...

Question

[dan79]

So I am analyzing strand-specific RNA seq data of Schizosaccharomyces pombe using Oases v0.2.06

I used ABySS to create kmer values of 34,36,38,...,64. When I try to use oases with a value > 31 I get this error message:

[0.000000] Velvet can't handle k-mers as long as 34! We'll stick to 31 if you don't mind.

Why is this? How do I get it to work with other higher kmer values?

Answer 1

[dan79]

Well if anyone cares I found the solution, you simply do

make 'MAXKMERLENGTH=92'

or whatever when you compile velvet and oases. Good luck!

Answer 2

[Lee Katz]

You have to recompile with a higher max k-mer length. Go to the velvet directory with the makefile and type

make ’MAXKMERLENGTH=57’

Or replace 57 with another larger odd number. Otherwise you are stuck with the default low number, 31.

Answer 3

[upendrakumar.devisetty]

I am trying to compile velvet to go a maximum k-mer length of "201" but velvet doesn't seem to respond to this. I am wondering is it possible to compile to that k-mer?

Thanks Upendra

[SES]

I would recommend you post this as a new question with some more information about what you tried and what went wrong. Otherwise, people will not see it at the bottom of this post.