NOVOPlasty Is there a single-end read workaround?

Is there a single-end read workaround?

Open srgill2 opened this issue 5 years ago • 5 comments

Jun 06 '19 03:06 srgill2

there is SE option, just forgot to change it in the config file, put SE in stead of PE Although it won't work as good as a PE library

Jun 06 '19 04:06 ndierckx

Ah, thank you. Any suggestions for optimizing it for SE and short reads? (~80bp average)

Jun 06 '19 18:06 srgill2

use a short kmer 23 For the rest you can't do that much

Jun 11 '19 02:06 ndierckx

Thanks, I've tried that and switching around other parameters without much luck. Is there any danger in dropping the kmer below 23?

Jun 11 '19 15:06 srgill2

Can go until 20 maybe, but if the dataset is not good enough it probably won't help

Jul 10 '19 02:07 ndierckx