I would like to know how to get the best quality reads and map them to a reference sequence. I have read this Fastq Quality Control Shootout among many other post. I have a pair ended sample and I want to get the high quality reads, what should I do ?
Also I would appreciate if you could comment on how to set the parameters for example for trimming look at this one mentioned in above post
perl TrimmingReads.pl -i data/s1.fq -l 10 -r 10 -o data/tmp.fq
Is it good to do this ?
I use FastQC on fastq files then I run the data through Trimmomatic, then run FastQC again, and then I compare to the original report to see how clipping modified the data.
what is the best way to do this? Trimmomatic or something else ?