reditools2

Identify A-to-I RNA editing in paired-read RNA sequencing BAM files using Reditools2

usage

nexus run --nf-workflow variant_calling_reditools2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --params_reditools2 "" \
    --params_reditools_annotatetable "-s 4 -c 1,2,3 -n gencode"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘rna_bam_file’, ‘rna_bam_bai_file’, ‘dna_bam_file’, ‘dna_bam_bai_file’
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--params_reditools2	reditools.py parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_reditools_annotatetable	Reditools AnnotateTable.py parameters (default: ‘“-s 4 -c 1,2,3 -n gencode”’). Note that the parameters need to be wrapped in quotes.