CLI parameters

rustar-aligner accepts STAR’s --camelCase parameter names. Defaults match STAR. This page lists the currently-supported parameters; if a parameter is missing, the binary errors out at startup rather than silently ignoring it.

Run rustar-aligner --help for the full machine-generated listing.

Run mode

Parameter	Default	Description
--runMode	alignReads	alignReads or genomeGenerate.
--runThreadN	1	Number of threads.
--runRNGseed	777	RNG seed for tie-breaking among equal-scoring alignments.

Genome

Parameter	Default	Description
--genomeDir	./GenomeDir	Path to the genome index directory.
--genomeFastaFiles	—	One or more FASTA files (required for genomeGenerate).
--genomeSAindexNbases	14	Length of the SA pre-indexing string (log2). Lower for small genomes.
--genomeChrBinNbits	18	Log2 of chromosome bin size.
--genomeSAsparseD	1	SA sparsity (higher = less RAM, slower mapping).

Read input

Parameter	Default	Description
--readFilesIn	—	Input FASTQ file(s); second file is mate 2 for paired-end (required for alignReads).
--readFilesCommand	—	Decompression command, e.g. zcat for .gz.
--readMapNumber	-1	Number of reads to map (-1 = all).
--clip5pNbases	0	Bases to clip from the 5’ end of each mate.
--clip3pNbases	0	Bases to clip from the 3’ end of each mate.

Output: file naming and format

Parameter	Default	Description
--outFileNamePrefix	./	Prefix (path + filename stem) for all output files.
--outSAMtype	SAM	SAM, BAM Unsorted, BAM SortedByCoordinate, or None.
--outBAMcompression	1	BGZF level. -1/0 = uncompressed; 1–8 = flate2 levels; ≥9 = max.
--limitBAMsortRAM	0	Max RAM (bytes) for sorted BAM. 0 = unlimited.
--outStd	None	Route primary output to stdout: None, SAM, BAM_Unsorted, BAM_SortedByCoordinate.

Output: SAM/BAM records

Parameter	Default	Description
--outSAMstrandField	None	None or intronMotif (sets XS tag from junction motifs).
--outSAMattributes	Standard	Tags to include: Standard, All, None, or an explicit list (e.g. NH HI AS NM nM MD).
--outSAMattrRGline	-	Read group line(s). Multiple blocks separated by a literal ,.
--outSAMunmapped	None	Unmapped reads in SAM: None, Within, or Within KeepPairs.
--outSAMmapqUnique	255	MAPQ value for uniquely-mapping reads.
--outSAMmultNmax	-1	Max alignments per read in SAM (-1 = all up to outFilterMultimapNmax).

Output: read filtering

Parameter	Default	Description
--outFilterType	Normal	Normal or BySJout (re-filter by discovered SJ pass).
--outFilterMultimapNmax	10	Max number of multi-mapping loci. Reads exceeding this are unmapped (MultiMapTooMany).
--outFilterMultimapScoreRange	1	Score range for keeping multi-mappers within best score.
--outFilterMismatchNmax	10	Max mismatches per pair.
--outFilterMismatchNoverLmax	0.3	Max ratio of mismatches to mapped length.
--outFilterScoreMin	0	Min absolute alignment score.
--outFilterScoreMinOverLread	0.66	Min alignment score normalized to read length.
--outFilterMatchNmin	0	Min absolute matched bases.
--outFilterMatchNminOverLread	0.66	Min matched bases normalized to read length.
--outFilterIntronMotifs	None	None, RemoveNoncanonical, or RemoveNoncanonicalUnannotated.
--outFilterIntronStrands	RemoveInconsistentStrands	None or RemoveInconsistentStrands.

Output: unmapped reads

Parameter	Default	Description
--outReadsUnmapped	None	None or Fastx (write Unmapped.out.mate1/mate2).

Output: splice junctions

Parameter	Default	Description
--outSJfilterOverhangMin	30 12 12 12	Min overhang per motif [noncan, GT/AG, GC/AG, AT/AC].
--outSJfilterCountUniqueMin	3 1 1 1	Min unique-mapping reads per motif.
--outSJfilterCountTotalMin	3 1 1 1	Min total reads per motif.
--outSJfilterDistToOtherSJmin	10 0 5 10	Min distance to other SJs per motif.
--outSJfilterIntronMaxVsReadN	50000 100000 200000	Max intron length per supporting-read count tier.

Alignment scoring

Parameter	Default	Description
--alignIntronMin	21	Min intron size (smaller gaps are deletions).
--alignIntronMax	0	Max intron size; 0 = auto from genome / win params.
--alignMatesGapMax	0	Max genomic distance between PE mates; 0 = auto.
--alignSplicedMateMapLmin	0	Min mapped length for spliced PE mate (absolute).
--alignSplicedMateMapLminOverLmate	0.66	Min mapped length for spliced PE mate (fraction).
--alignSJoverhangMin	5	Min overhang for novel splice junctions.
--alignSJDBoverhangMin	3	Min overhang for annotated junctions.
--alignSJstitchMismatchNmax	0 -1 0 0	Max mismatches for SJ stitching [noncan, GC/AG, AT/AC, noncan].

Scoring penalties

Parameter	Default	Description
--scoreGap	0	Canonical splice junction penalty.
--scoreGapNoncan	-8	Non-canonical junction penalty.
--scoreGapGCAG	-4	GC/AG junction penalty.
--scoreGapATAC	-8	AT/AC junction penalty.
--scoreDelOpen	-2	Deletion open penalty.
--scoreDelBase	-2	Deletion extension penalty per base.
--scoreInsOpen	-2	Insertion open penalty.
--scoreInsBase	-2	Insertion extension penalty per base.
--scoreStitchSJshift	1	Max score reduction for SJ stitching shift.
--scoreGenomicLengthLog2scale	-0.25	Log-scaled bonus per log2(genomicLength).

Seeds and windows

Parameter	Default	Description
--winReadCoverageRelativeMin	0.5	Min read coverage for an alignment window (fraction).
--winBinNbits	16	Log2 of window bin size for seed clustering.
--winAnchorDistNbins	9	Max bins for seed anchor distance.
--winFlankNbins	4	Bins to extend each window by on each side.
--winAnchorMultimapNmax	50	Max loci an anchor can map to.
--seedMultimapNmax	10000	Max loci a seed can map to.
--seedPerReadNmax	1000	Max seeds per read.
--seedPerWindowNmax	50	Max seeds per window.
--seedSearchStartLmax	50	Max distance between seed search start positions.
--seedSearchStartLmaxOverLread	1.0	seedSearchStartLmax normalised by read length.
--seedSearchLmax	0	Max seed length; 0 = unlimited.
--seedMapMin	5	Min mappable length for seed search termination.
--alignWindowsPerReadNmax	10000	Max alignment windows per read.
--alignTranscriptsPerWindowNmax	100	Max transcripts per window.

Splice junction database

Parameter	Default	Description
--sjdbGTFfile	—	GTF file with exon annotations.
--sjdbGTFchrPrefix	""	Prefix to add to chromosome names from GTF (e.g. chr).
--sjdbGTFfeatureExon	exon	GTF feature type to use as exon.
--sjdbGTFtagExonParentTranscript	transcript_id	GTF attribute for transcript ID.
--sjdbGTFtagExonParentGene	gene_id	GTF attribute for gene ID.
--sjdbOverhang	100	Overhang length around junctions in the index. Set to read_length - 1.
--sjdbScore	2	Extra score for alignments crossing annotated junctions.

Quantification

Parameter	Default	Description
--quantMode	—	GeneCounts and/or TranscriptomeSAM, space-separated.
--quantTranscriptomeSAMoutput	BanSingleEnd_BanIndels_ExtendSoftclip	Variant for transcriptome BAM: BanSingleEnd, BanSingleEnd_ExtendSoftclip, or the default RSEM-compatible form.

Two-pass mode

Parameter	Default	Description
--twopassMode	None	None or Basic.
--twopass1readsN	-1	Reads to use in pass 1 (-1 = all).

Chimeric detection

Parameter	Default	Description
--chimSegmentMin	0	Min chimeric segment length. 0 disables chimeric detection.
--chimScoreMin	0	Min total chimeric alignment score.
--chimScoreDropMax	20	Max drop in chimeric score vs read length.
--chimScoreSeparation	10	Min score separation for unique chimeric.
--chimMainSegmentMultNmax	10	Max multimapping for main chimeric segment.
--chimSegmentReadGapMax	0	Max read-space gap between chimeric segments.
--chimJunctionOverhangMin	20	Min overhang at chimeric junction.
--chimScoreJunctionNonGTAG	-1	Score penalty for non-GT/AG chimeric junctions.
--chimOutType	Junctions	Junctions, WithinBAM, or both space-separated.

Debug

Parameter	Default	Description
--readNameFilter	""	If set, only emit detailed alignment logs for reads with this name.