Issues

• [Bug]: Novel BambuTx#/BambuGene# IDs differ between identical runs

  GoekeLab/bambu#594 · Filter by author yinshiyi opened on Oct 6, 2026

• Bound peak memory in combineSplicedTranscriptModels() by keeping combined models in long form

  others
  Optimization

  GoekeLab/bambu#587 · Filter by author lingminhao opened on Aug 19, 2026 · user community pull request

• BiocParallel error

  GoekeLab/bambu#551 · Filter by author sophiachen1 opened on Apr 4, 2026
  3

• BiocParallel errors when running bambu

  GoekeLab/bambu#541 · Filter by author lyj95618 opened on Feb 12, 2026
  2

• which version of xgboost is ok?

  GoekeLab/bambu#539 · Filter by author lingfengxu opened on Feb 9, 2026
  1

• High NDR values when quantifying transposable elements in exosomes

  GoekeLab/bambu#536 · Filter by author NaixiangYu opened on Jan 29, 2026
  1

• error when using bambu to quantify SIRV

  GoekeLab/bambu#532 · Filter by author yinshiyi opened on Jan 20, 2026
  4

• Dependency issues when installing

  GoekeLab/bambu#523 · Filter by author sophiachen1 opened on Jan 11, 2026
  4

• Error while running bambu on single-cell long-read RNA-seq data

  GoekeLab/bambu#514 · Filter by author MapleLin-Bio opened on Dec 23, 2025
  1

• Error while running bambu on multiple samples

  GoekeLab/bambu#513 · Filter by author Motoufiq opened on Dec 4, 2025
  6

• questions about default NDR values if running in de novo mode

  GoekeLab/bambu#504 · Filter by author alexyfyf opened on Sep 9, 2025
  1

• Possibility to extend known gene models by adding UTRs

  GoekeLab/bambu#500 · Filter by author Annie-GW opened on Jun 26, 2025
  1

• Fusion Gene Analysis

  GoekeLab/bambu#498 · Filter by author mpizzagalli777 opened on Jun 24, 2025
  1

• Running out of memory from performing isoform discovery and quantification under low-memory mode

  GoekeLab/bambu#494 · Filter by author chingyinwan opened on Jun 17, 2025
  2

• error/crash for multisample merge across 98 samples

  GoekeLab/bambu#493 · Filter by author apsteinberg opened on Jun 13, 2025
  1

• plotBambu counts not explained

  GoekeLab/bambu#492 · Filter by author stfacc opened on Jun 10, 2025
  1

• [question]: Is it possible to run bambu with >2 conditions

  GoekeLab/bambu#491 · Filter by author tamuanand opened on Jun 9, 2025
  1

• BiocParallel error for sample

  GoekeLab/bambu#483 · Filter by author apsteinberg opened on May 18, 2025
  2

• Use of bambu with large plant genomes, splitted chromosome

  GoekeLab/bambu#478 · Filter by author gianmore opened on Apr 4, 2025
  1

• BiocParallel errors

  GoekeLab/bambu#477 · Filter by author C-Marcellus opened on Apr 2, 2025
  6

• invalid DNA letters

  GoekeLab/bambu#476 · Filter by author Geil625 opened on Apr 2, 2025
  6

• Question about single-cell requirements

  GoekeLab/bambu#475 · Filter by author TinyTasy opened on Mar 31, 2025
  3

• bambu missing novel isoform

  GoekeLab/bambu#472 · Filter by author lyj95618 opened on Mar 11, 2025
  3

• Two Isoforms with 4bp Difference

  GoekeLab/bambu#471 · Filter by author x1han opened on Mar 3, 2025
  2

• BiocParallel errors

  GoekeLab/bambu#468 · Filter by author abhijitcbio opened on Feb 27, 2025
  3