I have been practising with Trimmomatic for days but it is still not clear to me whether or not the paired output reads (in a pair-ended sequencing) are the ones needed for the downstream alignment.
Ciao Maria, Trimmomatic is not a Bioconductor package, and is not written in R Programming Language. This support forum is primarily for Bioconductor packages.
The paired output from Trimmomatic is what you should use for alignment. For more details, I suggest posting on Biostars, which is for more general bioinformatics topics/questions.
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