I try to understand the output files generated in kneaddata for a paired-end sample
Sample_1 (Forward) (11G)
Sample_2 (Reverse) (9.7G)
Sample_2.kneaddata.trimmed.single.2.fastq (86.3 MB)
I suppose that Sample_1.kneaddata.repeats.removed.1.fastq (and _2) are the files that I need to continue to the next step in the analysis, due to the file size (smaller than trimmed files). It is right?
Also, I don’t understand what is single in “Sample_X.kneaddata.trimmed.single.X.fastq” and why I obtain a so important difference between file size _1 (1.2G) and _2 (86.3MB)
I appreciate your help
All the best,