Pipeline for identifying miRNAs in small RNA sequencing data of mouse faecal samples
This pipeline requires the following packages:
cutadapt/1.8
bowtie/1.1.1
samtools/1.4
subread/1.6.0
And the following input files:
- demultiplexed small RNA sequencing data in compressed fastq format (suffix fastq.gz)
- tRNA reference file e.g. from GtRNAdb 2.0 --> http://gtrnadb.ucsc.edu
- rRNA reference e.g. from RNA central --> https://rnacentral.org
- mouse genome reference e.g. from --> https://www.ncbi.nlm.nih.gov
- mouse miRNA genome annotation file (mmu.gff3) e.g. from --> https://www.mirbase.org/download/
all reference files (not including the miRNA genome annotation file) need to be indexed prior to use using bowtie-build
e.g. bowtie-build <path_to_ref_fna_file> <path_to_output_file>
output file should have the suffix .ind
Please note that there may be newer versions of these packages that may contain bug fixes.
An R script for performing differential expression analysis of faecal miRNAs across conditions is also provided. This R script requires the prior install of DESEq2, dplyr and tidyverse to the R environment.