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

sample_Aligned.out.sam

Default output. SAM-format alignment file with header and records. Written when --outSAMtype SAM (the default).

sample_Aligned.out.bam

Unsorted BAM equivalent of Aligned.out.sam. Written when --outSAMtype BAM Unsorted.

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

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

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

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

Per-chunk progress lines emitted during alignment. Useful for monitoring long runs.

Splice junctions

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

Written when --chimSegmentMin > 0. Format depends on --chimOutType.

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

When --chimOutType includes WithinBAM, a chimeric read is written into the main BAM in place of its normal alignment, as STAR does: one segment as a normal record and the other as a supplementary record (FLAG 0x800, hard-clipped unless SoftClip), with SA tags linking the two. Paired reads whose mates lie on either side of the junction are written as two normal records. See the chimeric guide.

Quantification

sample_ReadsPerGene.out.tab

Per-gene read counts. Written when --quantMode GeneCounts is set. Four-column format:

gene_id    unstranded    forward_stranded    reverse_stranded

The 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

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

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

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.bam

The other output files (Log.final.out, SJ.out.tab, etc.) are still written to disk normally.