trim Illumina fastq reads to even read lengths

[wbsimey]

I have Illumina HiSeq fastq 1.9 files that have been quality trimmed. The sequence lengths range from 90 to 101 bp. I am using the Stacks pipeline, which requires equal length for all reads. Is there a simple way to trim the sequences in my files such that they are all 90bp long and control which end is trimmed? I have an Ubuntu 12 server.

PS. I am aware of the Stacks Process_radtags script, but for numerous reasons this script cannot process my data (multiple enzymes used, uneven barcode lengths and multiplexed different samples).

[dariober]

What about fastx_trimmer in the fastx toolkit (http://hannonlab.cshl.edu/fastx_tool...rimmer_usage)? In your case it should be something like:

fastx_trimmer -l 90 -i myseq.fastq -o myseq_even.fastq

Dario

[wbsimey]

Thank you Dariober, I installed Fastx tools and the trimmer worked perfectly, well, it worked after I figured out the -Q 33 option.