README.md

LR-tools - a toolkit for long read RNAseq data analysis

The pipeline performs several analyses that are suitable for barcoded reads.

Generic options
  --workflow           [string]  Type of analysis to be run (accepted: concatenate, reads-qc, reads-filter, chloroplast-contamination, genome-mapping,
                                 isoform-analysis)

Input/output
  --input_dir          [string]  Input directory containing samples to process
  --output_dir         [string]  Output directory where the results will be written

Reference genomes
  --genome_chl         [string]  Chloroplast genome (small file)
  --genome_nuc         [string]  Nuclear genome
  --genes              [string]  Genes in gtf format

Filtering parameters
  --phred_score        [integer] Phres score used to exclude reads [default: 7]

• concatenate: combined multiple fastq.gz files stored in directory. The name of the final gzip-ed file is the name of the top directory
• reads-qc: fastqc of each barcode
• reads-filter: filter reads by phred score
• chloroplast-contamination: perform chloroplast contamination screening. The final output includes stats
• genome-mapping: LR splice mapping on nuclear genome, includes counts analysis
• isoform-analysis:

Please use test/* data to run some examples.

Example module runs

The input directory is used for all the analysis types. Please remember to use pattern matching if the directory contains different types of files. Below are some more details

Create barcode files:

nextflow run ccdm/LR-toolkit -r main \
        -profile local,singularity \
        -resume \
        --input_dir "test/barcode*" \ # barcode* are directories containing fastq.gz files
        --workflow "concatenate" \
	--output_dir "results" \
	-with-singularity lr-tools.sif

Perform QC on reads

nextflow run ccdm/LR-toolkit -r main \
        -profile local,singularity \
        -resume \
        --input_dir "results/concat_barcoded/barcode*.fastq.gz" \ # input is fastq(.gz) reads. Can be either compressed or uncompressed files
        --workflow "reads-qc" \
        --output_dir "results" \
	-with-singularity lr-tools.sif

Check the presence of chloroplast sequences

nextflow run ccdm/LR-toolkit -r main \
        -profile local,singularity \
        -resume \
        --input_dir "results/concat_barcoded/barcode*.fastq.gz" \ # input is fastq(.gz) reads. Can be either compressed or uncompressed files
        --workflow "chloroplast-contamination" \
        --output_dir "results" \
	--genome_chl "/path/to/my/chl/genome.fasta" \
	-with-singularity lr-tools.sif

Map reads to reference genome

nextflow run ccdm/LR-toolkit -r main \
        -profile local,singularity \
        -resume \
        --input_dir "results/concat_barcoded/barcode*.fastq.gz" \ # input is fastq(.gz) reads. Can be either compressed or uncompressed files
        --workflow "genome-mapping" \
        --output_dir "results" \
        --genome_chl "/path/to/my/nucl/genome.fasta" \
	--genes "/path/to/my/genes/genes.gtf" \
	-with-singularity lr-tools.sif

Filter reads by phred score

nextflow run ccdm/LR-toolkit -r main \
        -profile local,singularity \
        -resume \
        --input_dir "results/concat_barcoded/barcode*.fastq.gz" \ # input is fastq(.gz) reads. Can be either compressed or uncompressed files
        --workflow "reads-filter" \
        --output_dir "results" \
	--phred_score 10 \
	-with-singularity lr-tools.sif