Issues

• Environment dependency conflicts during pipeline setup

  frattalab/PAPA#54 · Filter by author theammn opened on Jul 1, 2026

• APA event type and ribosomes

  frattalab/PAPA#53 · Filter by author K0ki116 opened on Dec 3, 2025

• Question about the novel_ref_combined.quant.last_exons.gtf

  frattalab/PAPA#52 · Filter by author MT2901 opened on Aug 12, 2025

• filter_tx_by_three_end - updating to atlas 3'end has unexpected(?) behaviour when polyA sites are intervals not single nucleotides

  low priority
  frattalab/PAPA#50 · Filter by author SamBryce-Smith opened on Jul 4, 2023

• get_combined_quant_gtf - retain matching reference transcript ID from novel GTF

  frattalab/PAPA#49 · Filter by author SamBryce-Smith opened on Jun 20, 2023

• NameError - name 'CONTRAST_NAME' is not defined if run_differential set to False

  frattalab/PAPA#48 · Filter by author SamBryce-Smith opened on Apr 26, 2023

• add script to combine novel last exons into single GTF to repo

  frattalab/PAPA#46 · Filter by author SamBryce-Smith opened on Mar 30, 2023

• update submit.sh to take config as command line argument & use conda prefix

  frattalab/PAPA#45 · Filter by author SamBryce-Smith opened on Mar 30, 2023

• Update code formatting for all scripts with black auto-formatter

  low priority
  frattalab/PAPA#42 · Filter by author SamBryce-Smith opened on Jan 3, 2023

• get_combined_quant_gtf.py - _ref suffix coordinates are for matching introns, should probably be removed

  low priority
  frattalab/PAPA#41 · Filter by author SamBryce-Smith opened on Jan 3, 2023

• 'label' for novel transcripts reported by StringTie is hardcoded in get_combined_quant_gtf.py

  low priority
  frattalab/PAPA#40 · Filter by author SamBryce-Smith opened on Nov 30, 2022

• Meta-issue - tidying up output GTFs

  frattalab/PAPA#37 · Filter by author SamBryce-Smith opened on Oct 13, 2022

• Intronic/'upstream' last exons - expand quantification regions to upstream penultimate exon/ shared region & add decoy transcripts

  enhancementhigh priority
  frattalab/PAPA#36 · Filter by author SamBryce-Smith opened on Oct 13, 2022
  1

• Remove/collapse duplicate transcripts from combined quantification GTF

  low priority
  frattalab/PAPA#34 · Filter by author SamBryce-Smith opened on Oct 13, 2022

• Check that number of event log messages count up excluding duplicates

  low priority
  frattalab/PAPA#14 · Filter by author SamBryce-Smith opened on Sep 7, 2021

• sge profile not working for UCL SGE cluster

  bug
  frattalab/PAPA#4 · Filter by author SamBryce-Smith opened on Jul 30, 2021