Potato_sRNA_analysis

🍠 small RNA analyses [S. tuberosum]

input

scripts

output

🌲 tree structure

Read more about scripts in ./scripts/README.md ❗

Read more about input/output in ./input/README.md ./output/README.md

📘📍Recommended sRNA data analysis pipeline / accompanying directories:

• 📂 Pre-processing # Known miRNAs identification

• 📂 Novel_miRNA_analysis # Novel miRNAs identification # Assigning the predicted miRNAs to known or novel MIR genes and families

• 📂 isomiRID # Identification of miRNA variants (i.e. isomiRs)

• 📂 phasiRNA_analysis # Identification of PHAS loci and phasiRNAs

• 📂 DEA # Differential expression analysis

• 📂 Target_prediction # sRNA target prediction

🔗 Useful bases:

• www.mirbase.org

• https://rnacentral.org/

• ftp://ftp.solgenomics.net

• http://solanaceae.plantbiology.msu.edu/

🔗 Useful tools:

• The small RNA group software for analysis and processing of NGS datasets

• UEA small RNA Workbench

• The ViennaRNA Package

• CD-HIT Suite

• GenomeTools

• FastQC or MultiQC

• FASTX-Toolkit

• SAMtools

• bedtools

• Cutadapt

• Bowtie and Bowtie2

• Mike Axtells' CleaveLand4 Mike Axtells' ShortStack

• de Oliveiras' isomiRID