- What you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling. In any case we do not recommend trimming as the bowtie2 parameters that we list will give accurate mapping information without trimming.
# fastqc_config:
# fastqc_theoretical_gc: "hg38_genome"
# extra_fn_clean_exts:
# - ".spikein.bowtie2"
# - "_processedFile"
# extra_fn_clean_trim:
# - "#"
# - ".myext"
# Customise the module search patterns to speed up execution time
# - Skip module sub-tools that we are not interested in
# - Replace file-content searching with filename pattern searching
# - Don't add anything that is the same as the MultiQC default
# See https://multiqc.info/docs/#optimise-file-search-patterns for details
