piRNA cluster annotation of non-model organisms

Question

[flogin]

Hi all,

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:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02141-w https://www.biorxiv.org/content/10.1101/2020.04.02.022509v1

Carried out the analysis citing the method of Brenneck et al. 2007:

https://pubmed.ncbi.nlm.nih.gov/17346786/

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?

Thanks.

Answer 1

[A. Domingues]

I would recommend that you look into the tools / DB provided by this group:

https://www.smallrnagroup.uni-mainz.de/

In particular the piRNA cluster database where there is information for at least one species of Mosquito (I did not make an extensive search). If the organisms you are interested in are not listed, check out their tool proTRAC which will predict piRNA clusters from mapped data.

NOTE: the group no longer exists, but there is no reason to believe the tools will not work for years to come - it's basically a collection of perl scripts - and the former PI, David Rosenkranz was always helpful in the past and might still be able to help with questions.

[flogin]

Thanks, I'll check this tools.

[flogin]

Dear A. Domingues,

thanks for this suggestion, I found the documentation and scripts that can be used in all steps of piRNA clusters analysis in smallrnagroup site. And the proTRAC tool in fact give the exact results that I was looking for.

Best,

[A. Domingues]

I am glad it helped :)