Issues

• Max supported python version?

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#324 · Filter by author bbimber opened on Jan 25, 2026

• Do not include dot character in track names

  bugImportant
  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#323 · Filter by author diekhans opened on May 25, 2025
  

• CAT doesn't carry over GENCODE tag information

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#322 · Filter by author diekhans opened on Jan 13, 2025

• Hello! I can't run it even on test data

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#321 · Filter by author VasyaSokolov opened on Jan 13, 2025

• CAT should handle internal exon expansions

  enhancement
  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#320 · Filter by author diekhans opened on Aug 1, 2024

• transMapPsl doesn't show base mismatches in browser

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#319 · Filter by author diekhans opened on Jun 19, 2024
  2

• Unable to run annotation pipeline. Target h2tg000040l block 10438982-10444550 exceeds sequence length 10441754

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#318 · Filter by author smkumaill opened on Apr 13, 2024

• CAT can't find gene duplications

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#317 · Filter by author DhakadPankaj opened on Mar 30, 2024

• Concensue bigGenePred column name incorrect

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#315 · Filter by author diekhans opened on Mar 9, 2024
  1

  

• CAT should not use Ensembl transcript names

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#309 · Filter by author diekhans opened on Feb 23, 2024
  

• CAT consensus track needs filters

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#308 · Filter by author diekhans opened on Feb 23, 2024
  

• Got exit code 1 (indicating failure) from job _toil_worker cgp file:/Comparative-Annotation-Toolkit/Darmor_A01_qwe/toil/augustus_cgp/jobStore kind-cgp/instance-cf_rpblx.

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#307 · Filter by author jwli-code opened on Jan 8, 2024
  1

• CAT T2T CHM13 GFF3 have gene_name mismatches between gene and transcript records

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#306 · Filter by author diekhans opened on Dec 11, 2023

• Error at filter_transmap.py

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#305 · Filter by author cbcunningham opened on Dec 6, 2023
  2

• TransMapPsl failed

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#303 · Filter by author DhakadPankaj opened on Oct 16, 2023

• Potential enhancements

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#302 · Filter by author ph09 opened on Aug 17, 2023

• Improve docker installation and docs

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#301 · Filter by author ph09 opened on Aug 17, 2023

• Error when running CAT with --augustus-cgp mode

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#296 · Filter by author peter-d-fields opened on Jul 7, 2023
  12

• CAT fails on cleanup when there are .nfs files

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#295 · Filter by author diekhans opened on Jul 6, 2023
  1

  

• ANNOTATION in the config file

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#294 · Filter by author GeorgeBGM opened on Jun 30, 2023
  3

• Capture stderr with Luigi

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#292 · Filter by author ph09 opened on Apr 24, 2023

• SF3B3 gene annotation missing in gff3

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#286 · Filter by author diekhans opened on Feb 28, 2023
  1

• Adjacent "exons" in GTF

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#285 · Filter by author diekhans opened on Feb 28, 2023

• CAT on AWS

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#284 · Filter by author larryns opened on Feb 20, 2023

• query regarding --ref-genome parameter

  ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#283 · Filter by author philge opened on Feb 19, 2023