StaticSection Alignment

After trimming, reads are aligned to a reference genome using bowtie2 version 2.2.6.

bowtie2 --dovetail --threads $threads -x [$index] -1 $fastq1 -2 $fastq2

• The term dovetailing describes mates which extend past one another, and is expected in CUT&RUN experiments. The --dovetail flag indicates that dovetailed alignments should be considered as concordant. See the bowtie2 documentation for an illustration of dovetailing.
• Mouse and human index files are available on the data portal.