Hi, I'm using gsAssembler 2.3 to assembly 450.000 reads. I have the xml autoTrimming variable set to false, but I can not bypass the trimming/screening step and the assembly is still using only 100.000 reads...why does this happen? Am I missing something?
Also I'm not giving any fasta by setting the screeningDatabase variable.
It seems like Newbler uses its own trimming database...is this true? how can I make gsassembler to use ALL reads i.e. whithout a screening process (at least more reads).
I believe the gsassembler 2.0 trims off less reads, 2.3 version only uses ~ 1/5 of all reads.
Thanks!
Also I'm not giving any fasta by setting the screeningDatabase variable.
It seems like Newbler uses its own trimming database...is this true? how can I make gsassembler to use ALL reads i.e. whithout a screening process (at least more reads).
I believe the gsassembler 2.0 trims off less reads, 2.3 version only uses ~ 1/5 of all reads.
Thanks!
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