[khmer] question re: trimmomatic/fastx

Fields, Christopher J cjfields at illinois.edu
Mon Feb 17 06:11:23 PST 2014

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 :)


More information about the khmer mailing list