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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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SNAP seed size #198

Open alephreish opened 8 years ago

alephreish commented 8 years ago

Transrate uses a fixed seed size of 23 for snap-aligner index which is the recommended optimum only for 100 nt reads. Would be great to have this argument either exposed to the user or calculated on the fly based on the read length, e.g.: max(RL*0.23, 17).

alephreish commented 8 years ago

As a workaround for now one can of course create the index himself before running transrate.

blahah commented 8 years ago

@har-wradim excellent point! We are going to be dropping SNAP in the next major version, but if we have several issues to address with a minor version release in the meantime I will include this.