star

Align paired-end RNA sequencing fastq files using STAR

usage

nexus run --nf-workflow alignment_star.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_star_genomegenerate "--genomeSAindexNbases 10 --sjdbOverhang 150" \
    --params_star "--genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --twopassMode Basic --chimSegmentMin 10 --chimOutType WithinBAM SoftClip Junctions --chimMultimapNmax 20 --chimOutJunctionFormat 0"

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’, ‘fastq_file_1’, ‘fastq_file_2’.
--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_star_genomegenerate	STAR genomeGenerate parameter (default: “--genomeSAindexNbases 10 --sjdbOverhang 150”). Note that the parameters need to be wrapped in quotes.
--params_star	STAR parameters (default: “--genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --twopassMode Basic --chimSegmentMin 10 --chimOutType WithinBAM SoftClip Junctions --chimMultimapNmax 20 --chimOutJunctionFormat 0”). Note that the parameters need to be wrapped in quotes.