After running Trimmomatic on a paired end PolyA RNA-seq dataset where both forward and reverse reads were in fastqsanger.gz format trimming the forward reads resulted in fastqsanger.gz files while trimming the reverse reads resulted in fastqsanger files. Q1. Is this normal output from the public Galaxy implementation of Trimmomatic? Q2. Can I simply uncompress the *.gz files so that both forward and reverse trimmed data sets are then ready for mappings (HISAT2)?
Thanks for any advice,
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