View Single Post
Old 05-20-2014, 08:10 PM   #4
punto_c
Member
 
Location: Japan, Tokyo

Join Date: Oct 2013
Posts: 11
Default

Hello Brian
First of all thank you for sharing your software
I am currently testing a few reads preprocessing tools (cutadapt, trimmomatic, fastx_tools and BBmap)

I can see from your post that is possible to quality trim PE reads in a single command:
bbduk.sh -Xmx1g in1=r1.fq in2=r2.fq out1=clean1.fq out2=clean2.fq minlen=25 qtrim=rl trimq=10

I was wondering if it possible to do that also for Trimming the adapters
Anyways, should I give for the quality trimming the files without the adapters?

sorry if some questions might look to simple to you but I am not experted in RAW reads processing yet

anyway, thanks a lot in advance for your kind reply

bests

Salvatore
punto_c is offline   Reply With Quote