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).
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).
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