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Environment dependency conflicts during pipeline setup

Status: Open.

#54 In frattalab/PAPA;

· theammn opened on Jul 1, 2026

APA event type and ribosomes

Status: Open.

#53 In frattalab/PAPA;

· K0ki116 opened on Dec 3, 2025

Question about the novel_ref_combined.quant.last_exons.gtf

Status: Open.

#52 In frattalab/PAPA;

· 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

Status: Open.

#50 In frattalab/PAPA;

· SamBryce-Smith opened on Jul 4, 2023

get_combined_quant_gtf - retain matching reference transcript ID from novel GTF

Status: Open.

#49 In frattalab/PAPA;

· SamBryce-Smith opened on Jun 20, 2023

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

Status: Open.

#48 In frattalab/PAPA;

· SamBryce-Smith opened on Apr 26, 2023

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

Status: Open.

#46 In frattalab/PAPA;

· SamBryce-Smith opened on Mar 30, 2023

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

Status: Open.

#45 In frattalab/PAPA;

· SamBryce-Smith opened on Mar 30, 2023

Update code formatting for all scripts with black auto-formatter

low priority

Status: Open.

#42 In frattalab/PAPA;

· 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

Status: Open.

#41 In frattalab/PAPA;

· SamBryce-Smith opened on Jan 3, 2023

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

low priority

Status: Open.

#40 In frattalab/PAPA;

· SamBryce-Smith opened on Nov 30, 2022

Meta-issue - tidying up output GTFs

Status: Open.

#37 In frattalab/PAPA;

· SamBryce-Smith opened on Oct 13, 2022