long-read-splicing

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name: long-read-splicing description: Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution. tool_type: mixed primary_tool: FLAIR

Version Compatibility

Reference examples tested with: FLAIR 2.0+, IsoQuant 3.5+, Bambu 3.4+, SQANTI3 5.2+, minimap2 2.26+, samtools 1.19+, rMATS-long 0.2+, IsoSeq3 4.0+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Long-Read Splicing Analysis

Full-length long-read sequencing solves problems that short-read AS cannot: anchor-length-limited microexon detection, complex multi-exon isoform deconvolution, recursive splicing in long introns, and transcript-quantification uncertainty in DTU. The 2024-2026 transition: long-read is becoming the splicing default for high-resolution analysis.

When Long-Read Wins

Question	Why long-read wins
Microexon detection (3-27 nt)	Reads span the microexon entirely; no aligner anchor problem
Long-intron recursive splicing	Can detect ratchet point usage (Sibley 2015 Nature)
Complex isoform deconvolution (TTN, MAPT, NEFM)	Single read per isoform avoids EM ambiguity
DTU without quantification uncertainty	Transcript identity is read-level, not inferred
Novel transcript discovery	No annotation dependence
Phasing splicing with SNVs	Allele-resolved isoforms
Single-cell full-length isoforms	MAS-Iso-seq + 10X 5' is the practical SOTA
Cryptic splicing in TDP-43 ALS	Full-length reads confirm cryptic exon inclusion in target transcripts

Platform Selection Matrix

Platform	Throughput	Accuracy (modal)	Best for	Fails when
PacBio Revio HiFi (Iso-Seq)	~25M reads / SMRT cell	Q30+ (CCS)	Bulk transcript discovery; gold standard	Cost prohibitive for very large cohorts
PacBio Kinnex / MAS-Iso-seq	~16x Iso-Seq via concatemer	Q30+	High-throughput single-cell long-read	Kinnex de-array (skera) is an extra step
ONT direct cDNA (R10.4.1, PCS-114)	Millions / flowcell	~98% simplex, ~99% duplex	Cost-effective; throughput	Minor higher error than HiFi
ONT direct RNA (RNA004, 2024+)	~30M reads	~96-98%	Native modifications (m6A, pseudo-U); no RT bias	Lower throughput; higher input
ONT pre-R10 (R9.4.1)	Same as R10	~85-90%	Legacy data	Pre-R10 not recommended for splicing analysis (false novel junctions)

Read length: PacBio HiFi cdna typically 1-10 kb; ONT cdna 0.5-50+ kb (long-tailed). Both span typical mammalian transcripts. Direct RNA on ONT preserves true 5'/3' termini and modifications.

Decision Tree by Use Case

Use case	Recommended tools
Bulk Iso-Seq transcript discovery in well-annotated organism	minimap2 -ax splice:hq -> IsoQuant or Bambu -> SQANTI3
Bulk ONT cDNA in well-annotated organism	minimap2 -ax splice -uf -k14 -> IsoQuant or FLAIR -> SQANTI3
End-to-end pipeline for differential analysis	FLAIR (correct -> collapse -> quantify -> diffSplice)
Joint discovery + quantification with calibrated novel rate	Bambu in R
De novo discovery for non-model organism	IsoQuant with --genedb omitted
Event-level differential splicing on long reads	rMATS-long
DTU on long-read transcript counts	DRIMSeq -> DEXSeq/satuRn -> stageR (no Salmon Gibbs needed)
Hybrid short+long for cohort	StringTie2 hybrid + FLAIR / IsoQuant
Single-cell full-length isoforms	MAS-Iso-seq + 10X 5' -> FLAMES or scNanoGPS
Cryptic exon validation in ALS	minimap2 -> FLAIR collapse -> manual inspection of UNC13A, STMN2
ASO design with full-isoform context	minimap2 -> IsoQuant -> SQANTI3 -> ASO design (see splice-variant-prediction)

Splice-Aware Alignment

# PacBio HiFi (Iso-Seq) -> minimap2 splice:hq preset
minimap2 -ax splice:hq -uf --secondary=no \
    -t 16 \
    reference.fa \
    isoseq.fastq.gz | \
    samtools sort -@ 8 -o isoseq_aligned.bam
samtools index isoseq_aligned.bam

# ONT direct cDNA (PCS-114, PCB-114): unstranded by default; omit -uf
minimap2 -ax splice -k14 \
    -t 16 \
    reference.fa \
    ont_cdna.fastq.gz | \
    samtools sort -@ 8 -o ont_cdna_aligned.bam
samtools index ont_cdna_aligned.bam

# ONT direct RNA (RNA004): truly stranded (RNA molecule preserves direction); -uf is correct
minimap2 -ax splice -uf -k14 \
    -t 16 \
    reference.fa \
    ont_rna.fastq.gz | \
    samtools sort -@ 8 -o ont_rna_aligned.bam
samtools index ont_rna_aligned.bam

-uf forces all reads to the forward transcript strand — correct for direct RNA (single-stranded) and stranded cDNA library preps; omit for unstranded cDNA (default ONT PCS/PCB kits) or ~half the reads are lost. --secondary=no discards secondary alignments. For genomes with poorly-annotated splice sites, supplement with --junc-bed gencode_junctions.bed. uLTRA (Sahlin & Mäkinen 2021 Bioinformatics) and deSALT (Liu 2019 Genome Biol) are alternatives with higher precision on small/cryptic exons.

Critical: splice:hq is the preset for HiFi (Q30+ reads); plain splice is for ONT regardless of cDNA vs direct RNA. Using splice on HiFi data underuses the high quality; using splice:hq on ONT misses true junctions due to error-tolerance mismatch.

FLAIR Workflow (correct -> collapse -> quantify -> diffSplice)

Goal: Identify, quantify, and test full-length isoforms from long-read RNA-seq across conditions.

Approach: Correct splice junctions against short-read or annotation evidence, collapse isoforms, quantify per-sample expression, run diffSplice for differential isoform usage.

flair correct \
    --query aligned.bed \
    --genome reference.fa \
    --gtf gencode.v45.annotation.gtf \
    --shortread short_read_junctions.bed \
    --output flair_corrected \
    --threads 16

flair collapse \
    --query flair_corrected_all_corrected.bed \
    --reads sample.fastq.gz \
    --genome reference.fa \
    --gtf gencode.v45.annotation.gtf \
    --output flair_collapsed \
    --threads 16

flair quantify \
    --reads_manifest reads_manifest.tsv \
    --isoforms flair_collapsed.isoforms.fa \
    --output flair_quantified \
    --threads 16

flair diffSplice \
    --isoforms flair_collapsed.isoforms.bed \
    --counts_matrix flair_quantified_counts.tsv \
    --conditions_table conditions.tsv \
    --output flair_diffsplice \
    --threads 16

FLAIR (Tang 2020 Nat Commun) handles ONT and PacBio with the same workflow. Output includes per-event PSI, FDR, and visual sashimi-like plots. The --shortread flag for flair correct is strongly recommended when short-read RNA-seq is available — it dramatically improves splice junction precision.

IsoQuant for Discovery + Quantification

Goal: De novo or annotation-guided isoform discovery and quantification with high precision.

Approach: Run isoquant.py with reference + reads + data type; output is GTF + counts.

isoquant.py \
    --reference reference.fa \
    --genedb gencode.v45.annotation.gtf \
    --fastq sample1.fastq.gz sample2.fastq.gz \
    --data_type pacbio_ccs \
    --output isoquant_output \
    --threads 16 \
    --model_construction_strategy default_pacbio

--data_type accepts pacbio_ccs (HiFi), nanopore (ONT), or assembly. As of v3.0+, --genedb is optional for de novo discovery. IsoQuant (Prjibelski 2023 Nat Biotech) is current SOTA for novel transcript reconstruction; pairs well with SQANTI3 for downstream classification.

Memory requirement: >=64 GB for atlas-scale runs.

Bambu for Annotation-Aware Discovery + Quantification

Goal: Joint discovery and quantification with statistical filtering of novel isoforms.

Approach: R Bioconductor package; takes BAM + reference annotation + genome; outputs ranged SE objects of known + novel transcripts.

library(bambu)

bam_files <- c('sample1.bam', 'sample2.bam', 'sample3.bam')
genome <- 'reference.fa'
gtf <- 'gencode.v45.annotation.gtf'

bambuAnnotations <- prepareAnnotations(gtf)

se <- bambu(
    reads = bam_files,
    annotations = bambuAnnotations,
    genome = genome,
    NDR = 0.1,
    ncore = 8
)

writeBambuOutput(se, path = 'bambu_output/')

tx_counts <- as.data.frame(assays(se)$counts)
gene_counts <- transcriptToGeneExpression(se)

Bambu (Chen 2023 Nat Methods 20:1187-1195) uses NDR (Novel Discovery Rate) as a single, calibrated parameter replacing per-sample heuristics:

NDR	Interpretation
0.05	Stringent; few novel transcripts; highest precision
0.1	Balanced (default)
0.2-0.3	Permissive; more novel discoveries; recall over precision

Excellent for combined discovery + quantification when statistical filtering matters.

SQANTI3 Classification

Goal: Classify discovered isoforms relative to reference; flag artifacts (intra-priming, RT-switching).

Approach: Run sqanti3_qc.py on the isoform GTF; review classification (FSM/ISM/NIC/NNC/antisense/genic/intergenic/fusion) and quality flags.

sqanti3_qc.py \
    isoforms.gtf \
    gencode.v45.annotation.gtf \
    reference.fa \
    --output sqanti3_qc \
    --aligner_choice minimap2 \
    --cage_peak refTSS_v3.3_human_coordinate.hg38.bed \
    --polyA_motif_list mouse_and_human.polyA_motif.txt \
    --cpus 8

sqanti3_filter.py rules \
    sqanti3_qc_classification.txt \
    --isoforms isoforms.fa \
    --gtf isoforms.gtf \
    --output sqanti3_filtered

SQANTI category	Meaning
FSM (Full Splice Match)	All junctions match reference
ISM (Incomplete Splice Match)	Subset of reference junctions
NIC (Novel In Catalog)	Novel combination of known junctions
NNC (Novel Not in Catalog)	Contains novel junction
Antisense	Overlaps gene on opposite strand
Genic	Within gene but no junction match
Intergenic	Between genes
Fusion	Spans multiple genes

SQANTI-LR (Pardo-Palacios 2024 Nat Methods) is the long-read-specific branch with QC tailored to ONT/PacBio error patterns. Filter intra-priming and RT-switching flags before reporting.

rMATS-long for Differential Isoform Analysis on Long-Read Data

Goal: Apply differential isoform analysis to long-read transcript abundance with classification and visualization.

Approach: rMATS-long is a multi-script Python pipeline distributed via bioconda; entry point is rmats-long followed by the script name. It supports two modes: abundance-based (using ESPRESSO-style abundance estimates) and ASM-based (Alternative Splicing Modules — sets of isoforms sharing exon-junction structure). Run preprocessing scripts in order before rmats_long.py.

conda install -c conda-forge -c bioconda rmats-long

# Preprocessing pipeline (ASM mode); per-script flag names verified vs Xinglab/rmats-long
rmats-long organize_gene_info_by_chr.py --gtf annotation.gtf --out-dir gene_info_by_chr/

# simplify_alignment_info processes one BAM at a time -> one TSV
for bam in *.bam; do
    rmats-long simplify_alignment_info.py --in-file "$bam" --out-tsv "alignment_info/${bam%.bam}.tsv"
done

# organize_alignment_info_by_gene_and_chr requires a samples-tsv (sample_id<TAB>tsv_path)
rmats-long organize_alignment_info_by_gene_and_chr.py \
    --gtf-dir gene_info_by_chr/ \
    --out-dir organized/ \
    --samples-tsv samples.tsv

rmats-long detect_splicing_events.py --align-dir organized/ --out-dir events/
rmats-long create_gtf_from_asm_definitions.py --event-dir events/ --out-gtf asm.gtf
rmats-long count_reads_for_asms.py --align-dir organized/ --event-dir events/ --out-dir asm_counts/

# Main differential analysis (ASM mode)
# Note: in ASM mode, --group-1 / --group-2 take sample IDs (matching the BAM basenames
# you organized into --align-dir); the BAM-to-counts step is done by count_reads_for_asms.py above.
rmats-long rmats_long.py \
    --group-1 ctrl1,ctrl2,ctrl3 \
    --group-2 trt1,trt2,trt3 \
    --event-dir events/ \
    --asm-counts-dir asm_counts/ \
    --align-dir organized/ \
    --gtf-dir gene_info_by_chr/ \
    --out-dir rmats_long_output/ \
    --adj-pvalue 0.05 \
    --delta-proportion 0.05 \
    --average-reads-per-group 10

# Alternative: abundance-based mode (when you already have ESPRESSO-style estimates)
rmats-long rmats_long.py \
    --abundance abundance.esp \
    --updated-gtf updated.gtf \
    --group-1 sample1,sample2,sample3 \
    --group-2 sample4,sample5,sample6 \
    --out-dir rmats_long_output/ \
    --no-splice-graph-plot

Key flags: --adj-pvalue (default 0.05), --delta-proportion (default 0.05), --average-reads-per-group (default 10), --no-splice-graph-plot (skip expensive splice-graph rendering).

rMATS-long is a separate tool from short-read rMATS-turbo. The predecessor lr2rmats used long reads only to augment the short-read rMATS GTF. The ASM framework treats AS as a set-of-isoforms problem, more natural for long-read data than rMATS-turbo's pre-defined event categories.

DTU on Long-Read Counts

Goal: Apply DRIMSeq + DEXSeq + stageR DTU pipeline to long-read transcript counts (no quantification uncertainty).

Approach: Use FLAIR or Bambu transcript counts as input; long-read counts are read-level identities, so no Salmon Gibbs samples needed.

library(DRIMSeq); library(DEXSeq); library(stageR)

counts <- read.table('flair_quantified_counts.tsv', header=TRUE, sep='\t')

samples <- data.frame(
    sample_id = c('s1', 's2', 's3', 's4', 's5', 's6'),
    condition = c('ctrl', 'ctrl', 'ctrl', 'trt', 'trt', 'trt')
)

d <- dmDSdata(counts = counts, samples = samples)
d <- dmFilter(
    d,
    min_samps_feature_expr = 3, min_feature_expr = 5,
    min_samps_feature_prop = 3, min_feature_prop = 0.1,
    min_samps_gene_expr = 6, min_gene_expr = 10
)

Then proceed with the standard DEXSeq + stageR DTU pipeline (see isoform-switching skill). IsoformSwitchAnalyzeR v2 has explicit long-read input support.

Single-Cell Long-Read for Splicing

Goal: Combine cell typing (10X 5' short read) with full-length isoform structure (Kinnex / MAS-Iso-seq).

Approach: Split 10X library; sequence half short-read for cell typing, half PacBio Kinnex for isoforms; recover cell barcodes from long reads via FLAMES or skera (Kinnex de-array).

# Demultiplex MAS-Iso-seq reads
skera split \
    raw_kinnex.bam \
    mas12_primers.fasta \
    demuxed.bam

# Then proceed with lima -> isoseq3 refine -> isoseq3 cluster pipeline
# For barcode rescue from FLAMES:
match_cell_barcode \
    --bam demuxed.bam \
    --barcodes 10x_barcodes.tsv \
    --output flames_demuxed.bam

Joglekar and colleagues used this approach for the mouse cortex isoform atlas (consult most recent publication for exact venue/year). See single-cell-splicing for tools that work on the demultiplexed data.

Per-Tool Failure Modes

minimap2: Wrong Preset

Trigger: Using -ax splice for PacBio HiFi (instead of -ax splice:hq) or -ax splice:hq for ONT.

Mechanism: Presets configure k-mer size, error tolerance, and indel scoring; mismatched preset is sub-optimal.

Symptom: Lower alignment rate; missed junctions on HiFi, false novel junctions on ONT.

Fix: splice:hq for HiFi; splice -k14 for ONT cDNA (unstranded); add -uf only for ONT direct RNA or stranded cDNA preps.

IsoQuant: Memory Pressure

Trigger: Atlas-scale cohort or low-RAM environment.

Mechanism: IsoQuant builds graph structures across all reads simultaneously.

Symptom: OOM kill; very slow runtime.

Fix: Increase RAM to >=64 GB; or batch by chromosome.

Bambu: NDR Mistuning

Trigger: NDR=0.5+ or NDR=0.01.

Mechanism: NDR controls the precision-recall tradeoff for novel transcripts.

Symptom: Too many spurious novel transcripts (high NDR) or missing real novel transcripts (low NDR).

Fix: Default NDR=0.1 is balanced; adjust based on validation expectations.

SQANTI3: RT-Switching Flags

Trigger: PacBio/ONT cDNA libraries with template switching artifacts.

Mechanism: RT-switching produces chimeric reads spanning two unrelated transcripts; SQANTI3 flags these.

Symptom: Many "fusion" transcripts in non-cancer samples; biologically implausible.

Fix: Filter out RT-switching flags via sqanti3_filter.py; investigate library prep if rate >5%.

FLAIR: Short-Read Augmentation Missing

Trigger: Running flair correct without --shortread.

Mechanism: FLAIR uses short-read junctions to correct long-read junction calls; without them, long-read errors persist as junction calls.

Symptom: Many false novel junctions; junction precision low.

Fix: Always include --shortread short_read_junctions.bed when short-read RNA-seq is available; generate with regtools junctions.

rMATS-long: GTF-Only Input

Trigger: Trying to give rMATS-long raw long-read BAMs.

Mechanism: rMATS-long expects per-sample isoform GTFs (from FLAIR/IsoQuant collapse), not raw alignments.

Symptom: Confusing parsing errors.

Fix: Run FLAIR/IsoQuant per sample first; pass the resulting GTFs.

Reconciliation: When Long-Read Tools Disagree

Pattern	Likely cause	Action
FLAIR has more isoforms than IsoQuant	FLAIR collapse less stringent; or IsoQuant filtered more aggressively	Both tools have valid pipelines; report based on use case
Bambu calls fewer novel than IsoQuant	Bambu NDR=0.1 is more conservative	Adjust NDR or trust Bambu's calibration
SQANTI3 classifies as NNC, FLAIR thinks FSM	GENCODE version mismatch	Verify both tools use same annotation
Long-read isoform calls don't match short-read events	Short-read EM ambiguity; or long-read coverage gap	Trust long-read for unambiguous; trust short-read for high-coverage events

Quality Control for Long-Read Splicing

Metric	PacBio HiFi	ONT cDNA R10.4.1
Read accuracy (modal)	Q30+ (>=99.9%)	~98% simplex / ~99% duplex
Splice junction concordance to short-read truth	~98%	95-98%
Median read length (transcripts)	1-4 kb	0.5-3 kb
Throughput per run	~25M HiFi reads	Tens of millions
Library input	100-500 ng total RNA	100-500 ng
Read direction	TSO + dT primed	TSO or random hexamer

Pre-R10 ONT (R9.4.1) had ~85-90% junction concordance and is no longer recommended for splicing.

Common Errors

Error	Cause	Solution
minimap2: too many anchors	Repeat-rich genome region	Use -N 50 to limit secondary alignments
IsoQuant: ssw-py not found	Missing dependency	pip install ssw-py
Bambu: prepareAnnotations failed	GTF malformed	Validate GTF with gffread -E
SQANTI3: kallisto not found	sqanti3 expects kallisto for short-read overlap	conda install -c bioconda kallisto
FLAIR: flair correct slow	Genome FASTA not indexed	samtools faidx reference.fa
skera: too many mismatches in adapter	MAS primer mismatch	Verify primer fasta matches kit version

Quality Thresholds

Metric	Recommendation	Source
Full-length non-chimeric (FLNC) %	>=80% (PacBio Iso-Seq)	PacBio convention
FSM%	>=50% in well-annotated genome (field-convention rule of thumb; not specified in the SQANTI paper)	SQANTI3 documentation; Tardaguila 2018 Genome Res 28:396
NNC%	<=30% (>30% suggests artifacts unless biologically interesting)	SQANTI3 convention
Junction support	>=2 reads (or >=3 with strict filtering)	Conservative
Bambu NDR	0.1 default; 0.05 stringent	Chen 2023 Nat Methods 20:1187
SQANTI3 RT-switching flag	filter out unless validated	SQANTI3 convention
SQANTI3 intra-priming flag	filter out	SQANTI3 convention
ONT R-version	R10.4.1+ for splicing	Splice junction concordance >=95% only with R10+
HiFi CCS passes	>=3	PacBio convention for Q30+

Common Pitfalls

• Ignoring reference annotation completeness — SQANTI3 NNC categorization differs by GENCODE version; report version with results.
• Not running isoseq3 refine — concatemers and polyA artifacts inflate isoform counts.
• Confusing FLAIR's 'collapse' with 'cluster' — collapse merges similar isoforms post-alignment; cluster (in isoseq3) merges raw reads pre-alignment.
• Treating ONT R9.x splice calls as reliable — pre-R10.4.1 error patterns generate false novel junctions.
• Skipping CAGE / polyA validation in SQANTI3 — TSS / TTS hallucination is common in long-read isoforms.
• DTU on too few replicates — long-read is expensive; n=2 vs n=2 is common but underpowered.
• PacBio HiFi alignment with -ax splice (not splice:hq) — use the HQ preset for HiFi data; default splice is for ONT.
• Skipping --shortread in FLAIR correct — long-read junction precision is much higher with short-read augmentation.

Related Skills

• splicing-quantification - Short-read PSI for cross-validation
• isoform-switching - DTU framework on long-read counts
• single-cell-splicing - MAS-Iso-seq + 10X integration
• long-read-sequencing/isoseq-analysis - PacBio Iso-Seq general pipeline (CCS, lima, refine, cluster)
• long-read-sequencing/long-read-alignment - minimap2 splice:hq details
• long-read-sequencing/long-read-qc - QC for long-read data
• splice-variant-prediction - Cross-reference variant predictions with full isoforms

References

• Tang et al 2020 Nat Commun - FLAIR
• Prjibelski et al 2023 Nat Biotech - IsoQuant
• Chen et al 2023 Nat Methods 20:1187-1195 - Bambu
• Tardaguila et al 2018 Genome Res - SQANTI (original)
• Pardo-Palacios et al 2024 Nat Methods - SQANTI3 / LRGASP benchmark
• Wyman et al 2020 bioRxiv - TALON (note: not formally peer-reviewed)
• Li 2018 / 2021 Bioinformatics - minimap2
• Sahlin & Makinen 2021 Bioinformatics - uLTRA
• Sibley et al 2015 Nature - recursive splicing
• Al'Khafaji et al 2024 Nat Biotech - MAS-Iso-seq / Kinnex
• Joglekar et al - scISOr-Seq2 mouse cortex (consult most recent publication for venue/year)
• Tian et al 2021 Genome Biology 22:310 - FLAMES
• Brown et al 2022 Nature - UNC13A cryptic exon (TDP-43)
• Klim et al 2019 Nat Neurosci - STMN2 cryptic splicing