What we can learn from FastQC reports

[Alexsongh]

Hi All,

I have a question: for a relatively "good" FastQC report, do we still need to do data pre-processing?

For example, my FastQC report has good adapter content, which shows 0. Do we still need to trim the adapters or filter the reads? Thank you!

[GenoMax]

FastQC is a quality assessment program. It does not change any data or do actual analysis.

If you are planning to do alignments against a good reference then you don't strictly need to do any trimming/filtering. Aligners will soft clip any adapter sequence that may still be present.

[Alexsongh]

Thank you for your reply! If I want to do assembly afterwards, do I need to trim and filter the reads? Thank you very much!