[khmer] question re: trimmomatic/fastx

[C. Titus Brown]

On Mon, Feb 17, 2014 at 02:11:23PM +0000, Fields, Christopher J wrote:
> On Feb 16, 2014, at 10:52 PM, "C. Titus Brown" <ctb at msu.edu> wrote:
> > 
> >> On Thu, Feb 13, 2014 at 04:09:51PM +0000, Fields, Christopher J wrote:
> >> Apologies in advanced if this is known, but I couldn?t find the answer on the list.  Is there any reason behind why trimmomatic is being using only for adaptor trimming, whereas fastx is used for quality trimming?  We?ve usually done this in a single trimmomatic run, something like:
> >> 
> >> java -jar /usr/local/bin/trimmomatic-0.30.jar PE ../SRR492065_?.fastq.gz s1_pe s1_se s2_pe s2_se \
> >>    ILLUMINACLIP:/usr/local/share/adapters/TruSeq3-PE.fa:2:30:10 \
> >>    TRAILING:30 \
> >>    LEADING:30 \
> >>    MINLEN:30
> > 
> > No reason, just what worked for us a few times.
> > 
> > Well, OK, I hate the Trimmomatic command line syntax... :) Would be happy
> > to move away from trimmomatic, frankly.
> > 
> > cheers,
> > --titus
> 
> Yup, agree there.  Okay, just checking to see if there were problems anyone encountered that we missed (we're a little paranoid :)

heh, nope! And please let us know if YOU encounter any problems that we
should know about.

(I think we need a trimming DSL.  More yak shaving, I'm sure, but...)

thanks,
--titus
-- 
C. Titus Brown, ctb at msu.edu