Issues

• orientation of soft-clipping reads should be considered

  murphycj/AGFusion#72 · Filter by author minw2828 opened on Oct 7, 2026

• support for GRCm39

  murphycj/AGFusion#71 · Filter by author mhoang22 opened on Sep 7, 2026

• Are the CDS blocks read in the right order for minus-strand genes?

  murphycj/AGFusion#70 · Filter by author Jackpepito opened on Sep 4, 2026

• Issue downloading ensembl 110 for AGFusion database

  murphycj/AGFusion#69 · Filter by author newtobioinfo opened on Jul 14, 2026
  1

• Add support for CTAT-LR-Fusion

  murphycj/AGFusion#64 · Filter by author hwismer opened on Nov 23, 2025

• Protein sequence of breakpoint within 5'UTR in the second partner gene is still buggy [Fix attached]

  murphycj/AGFusion#63 · Filter by author sufyazi opened on Oct 9, 2025

• plot error

  murphycj/AGFusion#62 · Filter by author anoronh4 opened on Jul 21, 2025
  1

• generic input for agfusion batch

  murphycj/AGFusion#61 · Filter by author kerstinth opened on May 2, 2025
  1

• Still getting a version 111 database error

  murphycj/AGFusion#60 · Filter by author mehlu22 opened on Apr 10, 2025
  1

• is the web app same as using code to annotate fusions

  murphycj/AGFusion#59 · Filter by author mehlu22 opened on Apr 10, 2025

• Fusion Transcript Annotation

  murphycj/AGFusion#58 · Filter by author pintoa1-mskcc opened on Oct 18, 2024
  1

• Bio.Alphabet no longer available

  murphycj/AGFusion#57 · Filter by author james-vincent opened on Sep 30, 2024
  1

• can we use AGFusion for annotating gene fusions detected in plant?

  murphycj/AGFusion#53 · Filter by author Fiza250 opened on Aug 7, 2023

• 5' UTR sequence not included when 3' gene junction is in 5' UTR

  bug
  murphycj/AGFusion#34 · Filter by author murphycj opened on Jun 15, 2020
  

• Frame issues

  murphycj/AGFusion#30 · Filter by author komalsrathi opened on Aug 22, 2019
  4

• Include exon number

  enhancement
  murphycj/AGFusion#12 · Filter by author murphycj opened on Jul 2, 2017
  1