bbduk for pre-processing

Question

[deepti1rao]

Please look at my raw and pre-processed reads. Pre-processing was done with bbduk. Parameters were as follows: qtrim=r trimq=20

Why is it trimming so severely for min Q 20? Can I change something?

[deepti1rao]

Links for raw and trimmed reads fastqc report:

https://ibb.co/kTMAHm

https://ibb.co/jwcsxm

Answer 1

[GenoMax]

Why is it trimming so severely for min Q 20

bbduk.shis doing what you asked it to do i.e. trim any data to the right once it encounters a region with average quality below 20. How many reads/bases were trimmed from the original?

If you are going to align to a reference there is no pressing need to filter based on quality. If you must, then use something like trimq=10. trimq=20 and above should only be needed if you were going to de novo assemble the data.

[deepti1rao]

Why have I lost bases with quality scores 20-32 as you can see in the uploaded pictures? How big is that window which is considered while looking for the avg quality?