Issues

• Unique count error skews counts between identical transcripts

  COMBINE-lab/oarfish#72 · Filter by author nadjano opened on Jul 23, 2026
  2

• How to quantify fusion transcripts and their parental transcripts

  COMBINE-lab/oarfish#67 · Filter by author Youpu-Chen opened on May 14, 2026

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

  COMBINE-lab/oarfish#64 · Filter by author VandaLovejoy opened on Mar 19, 2026

• Is oarfish able to distinguish endogenous from exogenous transcript?

  COMBINE-lab/oarfish#62 · Filter by author marionamujal opened on Feb 17, 2026

• transcriptome data aligned using dorado aligner

  COMBINE-lab/oarfish#61 · Filter by author lmulroney opened on Feb 4, 2026
  8

  

• Inferential Replicates of single cell model

  COMBINE-lab/oarfish#56 · Filter by author xhuashen opened on Dec 25, 2025
  3

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

  COMBINE-lab/oarfish#55 · Filter by author FenFotop opened on Dec 18, 2025
  1

• Difference in output between using bam and fastq as input

  COMBINE-lab/oarfish#54 · Filter by author lyj95618 opened on Dec 2, 2025
  7

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

  COMBINE-lab/oarfish#50 · Filter by author katsikora opened on Oct 2, 2025
  1

• Supporting pbmm2 for single-cell BAM files

  COMBINE-lab/oarfish#49 · Filter by author proteinosome opened on Sep 23, 2025
  15

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

  COMBINE-lab/oarfish#48 · Filter by author lirpa0 opened on Sep 3, 2025
  5

• Question: Oarfish suitable for Quantifying Haplotype-Resolved Transcriptomes

  COMBINE-lab/oarfish#33 · Filter by author nadjano opened on Oct 9, 2024

• Add option to use UMI information from BAM files (MI or RX tag)

  COMBINE-lab/oarfish#14 · Filter by author gringer opened on Mar 24, 2024