Output files
rustar-aligner produces the same set of output files as STAR. All files are written into the directory implied by --outFileNamePrefix, with names that match STAR’s exactly.
For the examples below, assume --outFileNamePrefix sample_. Replace sample_ with whatever you’ve configured.
Alignment output
Section titled “Alignment output”sample_Aligned.out.sam
Section titled “sample_Aligned.out.sam”Default output. SAM-format alignment file with header and records. Written when --outSAMtype SAM (the default).
sample_Aligned.out.bam
Section titled “sample_Aligned.out.bam”Unsorted BAM equivalent of Aligned.out.sam. Written when --outSAMtype BAM Unsorted.
sample_Aligned.sortedByCoord.out.bam
Section titled “sample_Aligned.sortedByCoord.out.bam”Coordinate-sorted BAM. Written when --outSAMtype BAM SortedByCoordinate. The sort happens in-memory by default; cap the RAM with --limitBAMsortRAM if needed.
sample_Aligned.toTranscriptome.out.bam
Section titled “sample_Aligned.toTranscriptome.out.bam”Transcriptome-coordinate BAM. Written when --quantMode TranscriptomeSAM is set. Each record’s reference is a transcript ID rather than a chromosome; one record is emitted per transcript that the read aligns within.
Log files
Section titled “Log files”sample_Log.final.out
Section titled “sample_Log.final.out”The summary statistics file — the most useful output for monitoring runs and feeding into MultiQC. Contains counts and rates for: input reads, uniquely mapped reads, reads mapped to multiple loci, reads mapped to too many loci, unmapped reads (with reasons), splice junctions, mismatch rates, deletion/insertion rates, and run timing.
Format is identical to STAR’s, so MultiQC parses it without modification.
sample_Log.out
Section titled “sample_Log.out”The verbose run log. Contains parameter values used, genome loading info, per-thread progress, and warnings. Useful when something looks wrong — search for WARNING or ERROR.
sample_Log.progress.out
Section titled “sample_Log.progress.out”Per-chunk progress lines emitted during alignment. Useful for monitoring long runs.
Splice junctions
Section titled “Splice junctions”sample_SJ.out.tab
Section titled “sample_SJ.out.tab”Tab-separated table of splice junctions discovered during alignment. STAR-compatible 9-column format:
| # | Column | Meaning |
|---|---|---|
| 1 | chr | Chromosome |
| 2 | start | Intron start (1-based) |
| 3 | end | Intron end (1-based) |
| 4 | strand | 0 = undefined, 1 = +, 2 = - |
| 5 | motif | 0 = non-canonical, 1 = GT/AG, 2 = CT/AC, 3 = GC/AG, 4 = CT/GC, 5 = AT/AC, 6 = GT/AT |
| 6 | annotated | 0 = novel, 1 = present in GTF / sjdb |
| 7 | unique_reads | Number of uniquely-mapping reads supporting the junction |
| 8 | multi_reads | Number of multi-mapping reads supporting the junction |
| 9 | max_overhang | Max overhang of any supporting read |
Filtered using the --outSJfilter* parameters (see CLI reference).
Chimeric output
Section titled “Chimeric output”Written when --chimSegmentMin > 0. Format depends on --chimOutType.
sample_Chimeric.out.junction
Section titled “sample_Chimeric.out.junction”14-column tab-separated table when --chimOutType includes Junctions (default). One row per chimeric junction. Format is STAR-compatible. See the chimeric guide for the full column breakdown.
Chimeric records in the primary BAM
Section titled “Chimeric records in the primary BAM”When --chimOutType includes WithinBAM, the chimeric segments are embedded as supplementary alignment records (FLAG 0x800) in the main BAM output, with SA tags linking the donor and acceptor halves. Tools like Arriba and STAR-Fusion know how to read either format.
Quantification
Section titled “Quantification”sample_ReadsPerGene.out.tab
Section titled “sample_ReadsPerGene.out.tab”Per-gene read counts. Written when --quantMode GeneCounts is set. Four-column format:
gene_id unstranded forward_stranded reverse_strandedThe first four rows are summary categories: N_unmapped, N_multimapping, N_noFeature, N_ambiguous. Subsequent rows are per-gene counts. Pick the column matching your library’s strandedness — see the quantification guide.
Unmapped reads
Section titled “Unmapped reads”sample_Unmapped.out.mate1 / sample_Unmapped.out.mate2
Section titled “sample_Unmapped.out.mate1 / sample_Unmapped.out.mate2”Written when --outReadsUnmapped Fastx is set. FASTQ output of every read that didn’t map (and reads that mapped to too many loci). Mate 2 is only present for paired-end input. For PE half-mapped pairs (one mate mapped, one not), both mates are written so the pair can be re-aligned later.
Two-pass mode
Section titled “Two-pass mode”In two-pass mode (--twopassMode Basic), pass 1 produces an internal _STARpass1/SJ.out.tab that’s used to seed pass 2. The final sample_SJ.out.tab reflects pass 2’s discoveries; pass 1’s intermediate file is not retained by default.
Standard output
Section titled “Standard output”When --outStd is set to SAM, BAM_Unsorted, or BAM_SortedByCoordinate, the corresponding alignment output is sent to stdout instead of a file. Useful for piping directly into samtools, sambamba, or any other downstream tool:
rustar-aligner --outStd BAM_Unsorted ... | samtools sort -@ 4 -o sample.sorted.bamThe other output files (Log.final.out, SJ.out.tab, etc.) are still written to disk normally.