Hi,
I am working with several assemblers to find the best one for my RNA-Seq data.
Besides Trinity and Oases I used SOAPdenovo -trans.
While Oases found massive sequences that have possible alternative splice products, SOAPdenovo-trans did not find a single one. I used 12 different k-mers from 19 to 89, e 1,3,5 and d 1,3,5 with all combinations. I allowed up to 10 alternative splicing products.
Is this behavior normal for this program?
Cheers,
Philipp
I am working with several assemblers to find the best one for my RNA-Seq data.
Besides Trinity and Oases I used SOAPdenovo -trans.
While Oases found massive sequences that have possible alternative splice products, SOAPdenovo-trans did not find a single one. I used 12 different k-mers from 19 to 89, e 1,3,5 and d 1,3,5 with all combinations. I allowed up to 10 alternative splicing products.
Is this behavior normal for this program?
Cheers,
Philipp
Comment