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Unique count error skews counts between identical transcripts

Status: Open.

#72 In COMBINE-lab/oarfish;

· nadjano opened on Jul 23, 2026

How to quantify fusion transcripts and their parental transcripts

Status: Open.

#67 In COMBINE-lab/oarfish;

· Youpu-Chen opened on May 14, 2026

How would genome realignment with minimap2 affect the analysis compared with transcriptome-aligned BAMs?

Status: Open.

#64 In COMBINE-lab/oarfish;

· VandaLovejoy opened on Mar 19, 2026

Is oarfish able to distinguish endogenous from exogenous transcript?

Status: Open.

#62 In COMBINE-lab/oarfish;

· marionamujal opened on Feb 17, 2026

transcriptome data aligned using dorado aligner

Status: Open.

#61 In COMBINE-lab/oarfish;

· lmulroney opened on Feb 4, 2026

Inferential Replicates of single cell model

Status: Open.

#56 In COMBINE-lab/oarfish;

· xhuashen opened on Dec 25, 2025

oarfish reports only shortest isoform despite long-read support for longer isoforms

Status: Open.

#55 In COMBINE-lab/oarfish;

· FenFotop opened on Dec 18, 2025

Difference in output between using bam and fastq as input

Status: Open.

#54 In COMBINE-lab/oarfish;

· lyj95618 opened on Dec 2, 2025

Question: can oarfish output be used with wasabi/sleuth for differential transcript expression?

Status: Open.

#50 In COMBINE-lab/oarfish;

· katsikora opened on Oct 2, 2025

Supporting pbmm2 for single-cell BAM files

Status: Open.

#49 In COMBINE-lab/oarfish;

· proteinosome opened on Sep 23, 2025

assigning almost all reads to longer of two overlapping isoforms (even though the reads visually map better to the short isoform)

Status: Open.

#48 In COMBINE-lab/oarfish;

· lirpa0 opened on Sep 3, 2025

Question: Oarfish suitable for Quantifying Haplotype-Resolved Transcriptomes

Status: Open.

#33 In COMBINE-lab/oarfish;

· nadjano opened on Oct 9, 2024