Splicing Analysis Pipeline

A nextflow pipeline of identifying and quantifying splicing events

Table of Contents

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1. Dependencies
2. File Format
   • Structure of input directories
   • Sample sheet
3. Usage
   • Run job
   • Usage options

Dependencies

• nextflow
• bwa
• hisat2
• samtools
• bamtools
• R packages
  • Rsamtools

File Format

Structure of input directories

Sample Sheet -- csv

sample	replicate	directory	read1	read2	reference
s1	rep1	/path/of/directory/	s1rep1_r1.fastq.gz	s1rep1_r2.fastq.gz	ref.fa
s1	rep2	/path/of/directory/	s1rep2_r1.fastq.gz	s1rep2_r2.fastq.gz	ref.fa
s1	rep3	/path/of/directory/	s1rep3_r1.fastq.gz	s1rep3_r2.fastq.gz	ref.fa

Note

1. The sample sheet must be a csv file and the header must be like below in the example

Usage

Run job

submit the bash script below

#!/bin/bash
#BSUB -o %J.o
#BSUB -e %J.e
#BSUB -R "select[mem>1000] rusage[mem=1000]"
#BSUB -M 1000
#BSUB -q normal

# modules
module load HGI/common/nextflow/23.10.0
module load HGI/softpack/users/fs18/nf_longread

#--------------#
# user specify #
#--------------#
# LSF group
export LSB_DEFAULT_USERGROUP=hgi

# Paths
export INPUTSAMPLE=$PWD/inputs/samplesheet.csv
export OUTPUTRES=$PWD/outputs

#-----------#
# pipelines #
#-----------#
nextflow run -resume nf_longread/main.nf --sample_sheet $INPUTSAMPLE \
                                         --protocol DNA \
                                         --platform hifi \
                                         --outdir $OUTPUTRES \
                                         --skip_snvcov

Usage options