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.