Bowtie2 error: skipping reads

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

Thank you

kneaddata bowtie02

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written 5.3 years ago by pdhrati02 •

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