I am trying to scaffold my contigs after using the Velvet Optimiser in Galaxy (Orione CRS4).
As I am inputting my parameters in SSPACE, I have come across a problem with parameter -m.
This parameter is for "minimum number of overlapping bases with the seed/contig during overhang consensus build up". Guides and manuals recommend to use a number that is close to your read length. For example, if your read length is 36bp, then they recommend using a number between 32 and 35 for -m parameter. My read length is 250 (based on FastQC results). I tried to use 247 for my parameter, however I encountered an error saying the maximum number I can use is 50. I know that if one uses SSPACE (using codes and stuff) outside of galaxy, you can bypass this limitation. Is there a way to get around this in galaxy?
Sorry if this post was confusing.