I have recently discovered BBTools and find it very intuitive use. However, as I am pretty new to processing raw sequence data, I haven't got my head around exactly how the quality trimming works in BBDuk. On the BBtools FAQs it states that trimq=10 will "... will quality-trim to Q10 using the Phred algorithm". However, I am unsure what this exactly means - does this trim reads with phred scores of 10 and below?
Specifically, what I noticed is that when I increase the trimq parameter (up to a point, e.g., at trimq=40 I end up with no reads) I increase the number of reads mapped to a reference genome. My understanding of this observation is that by setting a higher threshold for quality trimming, the probability of a read mapping to a reference genome increases. Is that the correct interpretation?
If it's helpful the reads are paired-end generated on Illumina MiSeq platform.
Any insight would be gratefully received!
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