Issues

• Transcripts with undefined GTF strand ('.') get inverted strand flags and reverse-complemented sequences in Aligned.toTranscriptome.out.bam, and lose their sense reads in STARsolo --soloStrand Forward

  alexdobin/STAR#2707 · Filter by author cindykrafft opened on Sep 24, 2026

• STAR genome index is not relocatable

  alexdobin/STAR#2706 · Filter by author ShiganLuo opened on Sep 16, 2026
  2

• Multiple --soloUMIdedup options break UniqueAndMult-*.mtx: extra records on feature index 1

  alexdobin/STAR#2704 · Filter by author danielsharritt opened on Sep 8, 2026

• Understanding ambiguous counts

  alexdobin/STAR#2702 · Filter by author Sgornard opened on Aug 19, 2026

• Difference between Gene and Velocyto

  alexdobin/STAR#2701 · Filter by author duzc-Repos opened on Jul 24, 2026

• STAR number of input reads | 0

  alexdobin/STAR#2700 · Filter by author bog197 opened on Jul 22, 2026

• BUG: different annotation status for the same junction while collapsing junctions (STARlong, deterministic)

  alexdobin/STAR#2695 · Filter by author alexdobin opened on Jun 29, 2026

• Provided: patch for big-endian support

  alexdobin/STAR#2690 · Filter by author pc297 opened on Jun 22, 2026
  3

• Unexplainable mapping output when using two genome assemblies in rice plant

  alexdobin/STAR#2688 · Filter by author vpbio opened on Jun 8, 2026

• Persistently add named FASTA sequences to an existing genome index

  alexdobin/STAR#2685 · Filter by author justinblethrow-cloud opened on May 17, 2026

• seeming inconsistency between CIGAR, nM, MD

  alexdobin/STAR#2684 · Filter by author tsgouros opened on May 8, 2026

• Effect of polyA trimming on STAR alignment and splice junction detection in paired-end RNA-seq

  alexdobin/STAR#2683 · Filter by author Mahsa-1380 opened on Apr 26, 2026

• Clarification on --quantMode TranscriptomeSAM behavior when using a custom GTF during mapping that differs from the index GTF

  alexdobin/STAR#2679 · Filter by author Ci-TJ opened on Apr 8, 2026

• STARsolo detects <200 cells from large 10x 3′ v2 dataset (expected thousands)

  alexdobin/STAR#2677 · Filter by author hu-jie-max opened on Mar 11, 2026
  1

• unmapped: other very high

  alexdobin/STAR#2675 · Filter by author elianaRo opened on Dec 25, 2025

• Alignment error

  alexdobin/STAR#2674 · Filter by author seandris1 opened on Dec 18, 2025

• STAR parameter --outSAMattrRGline when using STAR 2.7.9a

  alexdobin/STAR#2673 · Filter by author RobAlbn opened on Dec 4, 2025

• make fail star.cpp

  alexdobin/STAR#2672 · Filter by author snipershady opened on Nov 6, 2025
  1

• simulated data

  alexdobin/STAR#2671 · Filter by author 1690078218 opened on Oct 28, 2025

• Cannot build index

  alexdobin/STAR#2669 · Filter by author nguyen-ngoc-dat opened on Oct 22, 2025

• The newest version of STAR in bioconda channel can't receive any reads

  alexdobin/STAR#2668 · Filter by author falsetry1514 opened on Oct 21, 2025

• lot of multi-maaping-hg_38 genome mapping

  alexdobin/STAR#2667 · Filter by author Aastha2000tanu opened on Oct 17, 2025

• Sequencing saturation changed after adding --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts

  alexdobin/STAR#2665 · Filter by author Liripo opened on Sep 29, 2025

• GA fails on macOS due to Failed spawning readFilesCommand

  alexdobin/STAR#2663 · Filter by author eboileau opened on Sep 23, 2025
  8

• STAR/STARlong is not working with PacBio Isoseq reads

  alexdobin/STAR#2662 · Filter by author biofcallejas opened on Sep 19, 2025
  3