Hi everyone I have several questions about how to filter by quality scores. I am analyzing paired-end reads (Illumina) and I want to use qiime quality-filter q-score-joined.
1-I’m using the parameters with the default values but according to this post from illumina (https://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf)
“Q30 is considered a
benchmark for quality in next-generation sequencing”. Then should I continue with the default parameters or I better change --p-min-quality to 30 ?.
2- In this post from qiime https://docs.qiime2.org/2020.6/tutorials/qiime2-for-experienced-microbiome-researchers/ it says that “If for some reason your raw reads are not already all the same length, you’ll need to trim them to the same length before doing OTU clustering”.
But using quality-filter q-score-joined some reads will be truncated and these will be of different length, how can I solve that problem ?
3-If I use quality-filter q-score-joined is it necessary to use another type of filtering tool before as trimmomatic (apart from removing the primers) ?