I have few things to clarify.
1) I have a illumuna MiSeq dataset for a parasite genome. Machine itself gave paired-end reads as two separate datasets. one forward(R1) and other reverse(R2). When using FASTQC tool for one set e.g. filtering reads <70bp in R1 dataset, should we consider R1 as paired-end or no?
2) During quality trimming, I tried to adjust the sliding window size and see how per base quality improves. Increasing the sliding window size resulted in more aggressive trimming. I have selected sliding window 5, step 2 and quality<20 and filtered reads less than 70bp.
Appreciate any advice on this.