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:
- pair end read trimming
- quality analysis
- genome indexing and alignment
- miRDP2 miRNA identification
- separates sRNA from mRNA
- 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.
This code requires Bash >= 3.2 or Java >= 11
- Dependency download requires Miniconda, download here
- Download mirDeep2 using the instructions here
- 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
- 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
Jade Davis [email protected]