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Question: SSPACE scaffolder: -m parameter limited to 50
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gravatar for elin
3.6 years ago by
elin • 0
United States
elin • 0 wrote:

Hello,

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.

Thank you!
galaxy scaffolding sspace • 900 views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by elin • 0
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Parameters that are pre-set for tools on public Galaxy instances are often in place to manage server resources (whether these are the normal tool defaults - or others). That said, you could ask the administrators of this instance about a change. 

If that does not work out, moving to a local or cloud Galaxy where you can modify the settings yourself is the best path.
http://wiki.galaxyproject.org/BigPicture/Choices

Just be aware that adjusting certain parameters can trigger spikes in required resources. As a general rule, on any one server, a tool will execute (once the job is started) within Galaxy at the same rate and requiring the same resources as when run line-command. 

Best, Jen, Galaxy team
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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