How to set/choose the best parameter for fastq_quality_trimmer.
Ex: fastq_quality_trimmer -t ?? -l ?? -Q 33 -i input.fastq -o output trim.fastq.
It depends on your read length and QC report.
[-t N] = Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence).
[-l N] = Minimum length - sequences shorter than this (after trimming)
will be discarded. Default = 0 = no minimum length.
Suppose my read length is 100 bp, then I would like to trim the bases with quality score (-t) < 15 or 20, but not less than that. The more you increase the quality score, the more possiblity of getting high quality reads, but at the cost of losing not so bad reads.
Regarding minimum length (-l), I would consider at least the read to be at least 30 bases long.
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Is this a question? Can you please be more specific? What have you tried so far? What is your end goal, what are you doing with your sequence reads (assembly, mapping, etc.), and how stringent does your analysis have to be (no reference, quality of reference, etc.)?
HIi Josh,
I am going to map my RNA reads to human genome hg19, and after I checked my raw data using FastQC program, I found that my data need to be trimmed,so first I removed the adapter and I as I explained above I need to use fastq_quality_trimmer tool to trim the low quality sequence and I found the parameters -t ?? -l ?? -Q 33 so what is the criteria that should I use to for example put -t 20 -l 30 and Q33