I’m using Trimmomatic and I’m confused at what is it the 4 files it generates after I run it. I’m using paired end reads.
Trimmomatic says, “two files contain one read from each pair where both have survived filtering.” And the other two files contain “reads where one of the pair failed the filtering step”
Hi @galaxysab ,
Imagine, one read from a pair was filtered out (low quality, too short, for any reason). Usually, this is happen to reverse reads. In this situation the “partner” read will be recorded as not paired into these two additional files. As a result, Trimmomatic produces two files with only forward or reverse reads that lost the pair, in addition to files with properly paired reads.
Hope that helps.
Kind regards,
Igor