FastQC report

Question

[analyst]

How can I remove warnings for per base sequence content, per sequence GC content and sequence duplication levels using trimmomatic or fastp.

Thanks

Answer 1

[a.alnawfal.1992]

why would you remove warnings? FastQC provides a generic overview with pre determined threshold for both warning and failed, which might be not a failed for specific application. below is the command for fastp to trim your reads and you should modified it accordingly. trimmomatic would work too.

fastp -i input_forward.fq -I input_reverse.fq -o output_forward.fq -O output_reverse.fq -q 20 -u 30 -l 36 --cut_front --cut_tail --cut_window_size 4 --cut_mean_quality 20

I highly recommend not trimming a read unless you have a clear reason!

[analyst]

Thanks a.alnawfal.1992 !

Normally we trim when we have adapters or low quality reads. But in this scenario what do you suggest?

[a.alnawfal.1992]

Yeah, if you get some adapter or bad reads, without seeing the FastQC report, it is hard to judge the data. It is all about your application and what you are trying to achieve. In PCR-based applications, I would expect GC content to fail or show a warning due to the nature of the enrichment. However, I'll be happy if the amount of reads after deduplication is more than 80%, and I will keep an eye on the mean coverage.

It would be very helpful for us if you could post the FastQC report and explain a bit about your application.

NOTE: Personally, I prefer (and use) Fastp over FastQC.