Question Regarding Adapter Detection with fastp and Trimming with Trimmomatic
Is it methodologically appropriate to use fastp only for adapter detection and then perform the actual adapter trimming using Trimmomatic? In other words, is it acceptable to identify the adapter sequences with fastp first and subsequently provide those sequences to Trimmomatic for precise adapter removal, or would it be more appropriate to use a single tool for both detection and trimming?
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Arup Ghosh
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mahsa80.mm •
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mahsa80.mm •
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Why would you want to split the workflow like this?
If you use
fastpfor both, you will get a combined fastq quality report of before and after trimming. Also,fastpcan detect adapter sequences automatically.