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What we can learn from FastQC reports

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  • What we can learn from FastQC reports

    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!

  • #2
    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.

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    • #3
      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!

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