Combo-seq

Combo-seq is an analysis program which can process raw FASTA/FASTQ sequencing reads produced using the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit. It performs:

1. pair end read trimming
2. quality analysis
3. genome indexing and alignment
4. miRDP2 miRNA identification
5. separates sRNA from mRNA
6. creates a gene count matrix which can be used for further differential expression analysis.

Usage of this pipeline on input reads prepared using the Combo-Seq kit presents a workflow for sRNA/mRNA combined analysis which replaces the tradtional need to separetly analyse mRNA and sRNA samples, reducing cost and time input.

Getting Started

This code requires Bash >= 3.2 or Java >= 11

1. Dependency download requires Miniconda, download here
2. Download mirDeep2 using the instructions here
3. Run the following (or equivalent) in an empty directory to download workflow and dependancies:

$ git clone https://github.com/jadedavis5/combo-seq
$ cd combo-seq/
$ bash installdep.sh

3. Running the pipeline:

$ nano workflow.nf

# change parameters to desired input 
params.genome_file = "/path/to/genome.fa"
params.gtf_file = "/path/to/genome.gtf"
params.outdir = "/path/to/outdirectory"
params.reads = '/path/to/raw/reads/fa'
params.miRDP2 = "/path/to/miRDP2-download"

#also change adpaters in process TRIM to desired 

#run using:
$ nextflow run workflow.nf

#if the run is interrupted, resume from last point using:
$ nextflow run workflow.nf -resume

Contact

Jade Davis 20558259@student.curitn.edu.au