Hi I am going to make a reliable draft genome of a cultured bacteria. This is my FastQC report on Miseq reads from a genome sequencing project of bacteria prior to any trimming:
The original sequencing is a paired end but to focus on my problem, here I just put the QC of the forward (-->) direction. the other one has the same problem too. Quality trimming based on Q20 with Sickle, gives this:
Which I thought was not fine yet, so I used FastX and awk command to trim for 18n from the beginning and after 200 n length form the end of all reads and 194 n for the problematic tile 2117. then I applied the q20 and other default setting for final trimming with Sickle. this is the out put:
Isn't that too much of trimming? is this necessary to go that far? there are still warnings in some parts like sequence duplication level or kmer content. should I go further to solve this warnings? are they important in my case?