Hi, All,

I have a question of how to set up a quality filter which only applies to the first 3 bases at 5' ends of my reads. I want to set up a threshold (i.e. Quality score 20) so that if any reads in my input FASTQ file which have any of the first 3 bases below the threshold will be discarded or removed from the output file. I tried Cutadapt quality trimming on 5' end of reads, and I found that Cutadapt only trim the low-quality bases on 5' ends, but not discarding these reads in the output file. I also know there is a quality filter tool in Fastx-toolkit, but from the manual, I can see it only has two options that 1: [-q N] = Minimum quality score to keep; and 2: [-p N] = Minimum percent of bases that must have [-q] quality. I do not think these two options in Fastx-toolkit are helping in my case as I only care the quality score of the first 3 bases at the 5' ends of my reads.

Is there a tool which could help in my case? I'd appreciate if you could give me any input.

Best,

Xiao