This repository contains the data and code associated with the following manuscript:

MicroRNAs are deeply linked to the emergence of the complex octopus brain
Grygoriy Zolotarov, Bastian Fromm, Ivano Legnini, Salah Ayoub, Gianluca Polese, Valeria Maselli, Peter J. Chabot, Jakob Vinther, Ruth Styfhals, Eve >Seuntjens, Anna Di Cosmo, Kevin J. Peterson, Nikolaus Rajewsky
bioRxiv 2022.02.15.480520; doi: https://doi.org/10.1101/2022.02.15.480520

Genome annotation

Genome annotation files are stored in genome_annotation folder.
Octopus_sinensis_annotation.gtf.zip - genome annotation obtained in the study.
isoforms_TAMA_polished.fa.zip - mRNA isoforms generated from Iso-Seq and FLAM-seq data using TAMA with a polishing step.

Gene extension

This folder contains a Snakemake pipeline used to extend genes with FLAM-seq data. This pipeline starts with an FLAM-seq data collapsed into a single .bam file. Then:

1. Cleavage sites are extracted from FLAM-seq reads ("tags").
2. The tags are next merged and assigned to individual genes from a .gtf file.
3. The last exons of the genes are extended and added to annotation file.
   For more information, vis README.md file in a corresponding directory.

How to cite

If you use the code or data from this repository, please cite:

• Preprint: Zolotarov, biorXiv 2022.