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). Several files per mate are comma-separated (a_1.fq,b_1.fq a_2.fq,b_2.fq) and read in order; each mate must list the same number. Compression is detected from the file contents (gzip; bzip2/zstd/xz with the matching build features) unless --readFilesCommand is given. A --soloType run appends the barcode read as the last file: cDNA_read barcode_read, or cDNA_read1 cDNA_read2 barcode_read for paired-end cDNA.
--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, BAM Unsorted SortedByCoordinate (both files), or None.
--outBAMcompression	1	BGZF level. -1/0 = uncompressed; 1–8 = flate2 levels; ≥9 = max.
--limitBAMsortRAM	0	Max RAM for the coordinate sort; accepts a suffix (8G, 512M). Records beyond it spill to sorted runs beside the output and are merged, so output is unaffected by this value. 0 means 512 MiB. Very small values still work but cost wall time (many spill runs plus an extra merge pass).
--outStd	None	Send one output to stdout instead of its file: SAM, BAM_Unsorted or BAM_SortedByCoordinate, each only when that output is requested by --outSAMtype. None writes everything to files.

Output: SAM/BAM records

Parameter	Default	Description
--outSAMstrandField	None	None or intronMotif: adds the XS tag, from the junction strands of the whole alignment (both mates of a pair), and drops spliced alignments whose strand is undefined. Listing XS in --outSAMattributes turns it on, as in STAR.
--outSAMattributes	Standard	Tags to include, written in the order given: Standard (NH HI AS nM), All (NH HI AS nM NM MD jM jI MC ch), None, or a list of NH HI AS nM NM MD jM jI MC ch XS RG vA vG vW, plus the STARsolo tags CR CY UR UY CB UB GX GN gx gn sM sS sQ sF. Derived tags follow the list: RG (read group), XS (intronMotif), vW (WASP), then NM (--chimOutType WithinBAM). ch, vA, vG, vW and the STARsolo tags need BAM output, so All does too; CB/UB need --outSAMtype BAM SortedByCoordinate. Unmapped records always carry NH HI AS nM uT (then RG, then any requested STARsolo barcode tags in the fixed order CR CY CB UR UY sM sS sQ, and CB UB in the sorted BAM); the transcriptome BAM carries NH HI (then RG).
--outSAMattrRGline	-	Read group line(s). Multiple blocks separated by a literal ,: one per --readFilesIn file, or a single one for all files.
--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. With BySJout, reads with an unannotated junction are held until every read is mapped, then mapped again with only the novel junctions that passed the --outSJfilter* filters, and written after the others (STAR’s two stages).
--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; may be gzipped (STAR needs plain text).
--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.
--sjdbInsertSave	Basic	After junctions are inserted at mapping (GTF at mapping or two-pass): Basic writes the junction and transcript tables to <prefix>_STARgenome/, All also writes Genome, SA and SAindex.
--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.
--quantTranscriptomeUnspliced	None	rustar-aligner extension. Intron / PreMRNA: add one unspliced target per gene (<gene_id>-I: merged introns plus flanks, or the gene body) to the transcriptome BAM. None is STAR’s behaviour. See Bulk total RNA-seq.
--quantTranscriptomeUnsplicedFlank	-1	rustar-aligner extension. Flank around each merged intron for Intron; -1 uses the index’s sjdbOverhang.
--quantTranscriptomeUnsplicedFasta	No	rustar-aligner extension. Yes writes the unspliced target sequences to Aligned.toTranscriptome.unspliced.fa.
--quantGeneSplicing	No	rustar-aligner extension. Yes writes bulk spliced / unspliced / ambiguous gene counts (ReadsPerGeneSplicing.out.tab), see Bulk total RNA-seq.
--outSAMsplicingStatus	No	rustar-aligner extension. Yes adds an sp:A splicing-status tag (S / U / A) to genomic SAM/BAM records.
--quantGeneCoverage	No	rustar-aligner extension. Yes writes per-gene exonic coverage to GeneCoverage.out.bin for DegNorm. See DegNorm.
--degNormSampleId	basename of --outFileNamePrefix	rustar-aligner extension. Sample name stored in GeneCoverage.out.bin.
--degNormCoverageFiles	—	rustar-aligner extension. Two or more GeneCoverage.out.bin files: runs the DegNorm merge (no reads, no --runMode) and writes DegNorm.out/. Tuning: --degNormIter, --degNormNmfIter, --degNormDownsampleRate, --degNormMinimaxCoverage, --degNormSkipBaselineSelection, --degNormBins, --degNormMinHighCoverage (see the guide).
--soloCellRangerSummary	No	rustar-aligner extension. Yes writes Solo.out/<feature>/CellRanger.summary.csv for Gene and GeneFull (both needed): the fractions of all reads that map uniquely in exonic, intronic or intergenic regions, or antisense to a gene, under CellRanger’s metric names. STARsolo’s Summary.csv is unchanged.

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 and/or WithinBAM, optionally followed by HardClip (default) or SoftClip for the supplementary segment. WithinBAM requires --outSAMtype BAM.

Debug

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