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  • Do I need to run trim galore even if my reads are of good quality?

    Hi,

    I am a beginner in the field of genomics. So I have one doubt should I use trim galore to trim my sequence even if they are of good quality?

    From the fastqc result I have I can say that all of them have "per base sequence quality" more than 29.

    So is it required to run trim galore, just to remove the adapter sequence?

    Thanks.

  • #2
    I guess this would depend on the type of experiment at hand, as some applications are a bit more forgiving than others. If you wanted you could run Trim Galore (and or your alignment method of choice), look at the trimming (and/or alignment) stats and decide then whether it was worth it. Since long read lengths tend to coincide with adapter contamination we trim all sequences by default these days.

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