The last thing trimmomatic expects to see is the trimming parameters: : Output file that contains orphaned reads from the _2 file.: Output file that contains surviving pairs from the _2 file.: Output file that contains orphaned reads from the _1 file.: Output file that contains surviving pairs from the _1 file.Typically the file name will contain an _2 or _R2 in the name Typically the file name will contain an _1 or _R1 in the name In paired end mode, Trimmomatic expects the two input files, and then the names of the The flags are followed by positional arguments, meaning the order in which you specify them is important. These flags are not necessary, but they can give you more control over the command. ![]() For example, you can specify threads to indicate the number processors on your computer that you want Trimmomatic to use. Next, we specify what flag we would like to run. ![]() This output shows us that we must first specify whether we have paired end ( PE) or single end ( SE) reads.
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