Simple request and my apologies if I missed this and its already implemented. But right now I think only fasta is handled. But there are many scenarios where it would streamline things if trf was fastq aware. Illumina have an option "--fastq-n-quality" so you can set the quality score for any bases converted to N which would also be useful to have.
Adrian
Simple request and my apologies if I missed this and its already implemented. But right now I think only fasta is handled. But there are many scenarios where it would streamline things if trf was fastq aware. Illumina have an option "--fastq-n-quality" so you can set the quality score for any bases converted to N which would also be useful to have.
Adrian