I'm reading about the annotation of cluster piRNAs, more precisely with piRNA clusters of mosquitoes.
For model organisms, such as human, drosophila and Mus musculus, for example, we found some pipelines, but for non-model, it's quite difficult...
The 2 latest works with mosquitoes:
Carried out the analysis citing the method of Brenneck et al. 2007:
That is basically:
"All piRNAs except the 10% of reads corresponding to miRNAs, rRNAs, tRNAs, other ncRNAs, and the sense strand of annotated genes were mapped to Release 5 and the telomeric X-TAS repeat L03284. Nucleotides corresponding to the 5′ end of each piRNA were weighted according to N/M with N = cloning frequency and M = number of genomic mappings. We used a 5 kb sliding window to identify all regions with densities greater than 1 piRNA/kb. Windows within 20 kb of each other were collapsed into clusters. Clusters with at least 5 piRNAs that uniquely matched to the cluster were retained."
This study didn't explain how they did that, if they used one specific tool or an in house script.
Someone here already studied that, and know how can I pick the bowtie2 output and execute these steps?