Two reference modes
Quantify transcriptome-aligned BAMs directly or reconstruct transcript models from genome + GTF/GFF/GFF3.
RNAQuant v0.1.4
Transcript-level counts from BAM files.
RNAQuant converts BAM alignments into transcript-level fragment counts. It accepts transcriptome-aligned BAMs with a transcript FASTA or genome-aligned BAMs with a genome FASTA and GTF/GFF/GFF3, and produces per-sample plus combined count/TPM matrices.
What it does
RNAQuant workflow.
Purpose-built scientific software with downloadable documentation and reproducible local workflows.
Whole-number counts
Raw and EM-estimated transcript counts are exported as integers, with TPM available separately.
Multimapper EM
Deterministic batch EM uses abundance, effective length and alignment evidence to distribute multimapping fragments.
Low-memory browser
v0.1.4 streams BGZF blocks and uses IndexedDB QNAME buckets instead of loading complete BAMs into RAM.
Multi-sample integrity
Immutable sample snapshots and total-count checks protect combined matrices from state/export corruption.
Gene mapping
Optional transcript-to-gene tables add gene_id/gene_name while preserving transcript-level counting.
Usage
CLI examples.
Transcriptome mode requires a transcript FASTA; genome mode additionally requires annotation:
rnaquant --bam A.bam B.bam \ --transcriptome transcripts.fa \ --transcript-gene-map tx2gene.tsv \ --output-dir rnaquant_out # Genome mode rnaquant --bam A.bam B.bam \ --genome GRCh38.fa --annotation gencode.gtf \ --output-dir rnaquant_out
Install / launch
Start the release locally.
tar -xzf RNAQuant_CLI_v0.1.4_linux_x86_64.tar.gz cd RNAQuant_CLI_v0.1.4_linux_x86_64 chmod +x rnaquant ./rnaquant --help
Research-use software. RNAQuant is a development research release. Review run_summary.tsv and reference/strand settings before downstream differential-expression analysis.