I have a PE illumina miseq data set (separate forward-R1 & reverse-R2) of a WGS of a parasite. I'm using a local instance of galaxy. I have run FASTQC on sequencer given data sets and decided to do some quality control since quality drops towards the end of reads.
I have few doubts to clear and appreciate if galaxy team or anyone in the forum could help me to solve them.
1) According to FASTQC I decided to quality trim reads using FASTQ quality trimmer (sliding window=5, step=2, avg quality=20). Since quality degrades towards 3' end should I trim 3' end only. Is this Ok?
2) I have seen suggestions to perform quality control for PE data sets (R1 & R2) together & not separately. Isn't it correct to perform QC on R1 & R2 separately?
3) If so, I have to use another tool instead of FASTQ quality trimmer. Would it be a good option to use trimmomatic or Trim galore?
4) Later I used Filter FASTQ to filter reads <70bp; If I use R1 dataset only should I use yes/no to "This is paired end data" option? Can I select multiple data sets option in filter FASTQ to choose both R1&R2 together?
Thanks in advance, Sumudu