Hi BFM,
I used Trimmomatic to trim for adapters and quality (collect orphaned reads). Imported this into CLC Genomics server to remove chloroplast aligning reads and duplicate reads (again collect orphans). Export as .fastq and run Trimmomatic again to remove reads <20 bp - I also trimmed to max 200 bp as I was finding some bias towards the ends of reads.
I hope that helps.
I used Trimmomatic to trim for adapters and quality (collect orphaned reads). Imported this into CLC Genomics server to remove chloroplast aligning reads and duplicate reads (again collect orphans). Export as .fastq and run Trimmomatic again to remove reads <20 bp - I also trimmed to max 200 bp as I was finding some bias towards the ends of reads.
I hope that helps.
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