Hi all, I am using kneaddata with bowtie2. Using the default parameters with trimmomatic options (trimmomatic_options = MINLEN:12 SLIDINGWINDOW:4:15) my log file showed warnings of the following type repeating several times:
Warning: skipping read '####' because length (1) <= # seed mismatches (0) Warning: skipping read '####' because it was < 2 characters long
But when I use kneaddata with default parameters I do not get this warning, however, end up getting fewer reads as compared to using the modified parameters.
I have the following questions:
Does this mean there is a problem with my reads? If so how to find that out? Should I avoid using trimmomatic? Do you think that can cause the reads to be filtered out here? Will I lose these reads in the next steps to come?
Any help would be appreciated