frattalab/PAPA

View on GitHub

PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data

Stars: 2
Forks: 0
Open beginner issues: 0
Indexed issues: 16

Dominant language: Python
License: GPL-3.0
Last GitHub push: Apr 14, 2025
Latest indexed: Sep 16, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

16 open issues indexed

sge profile not working for UCL SGE cluster Open

bug

frattalab/PAPA#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Check that number of event log messages count up excluding duplicates Open

low priority

frattalab/PAPA#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Remove/collapse duplicate transcripts from combined quantification GTF Open

low priority

frattalab/PAPA#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Intronic/'upstream' last exons - expand quantification regions to upstream penultimate exon/ shared region & add decoy transcripts Open

enhancement high priority

frattalab/PAPA#36 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Meta-issue - tidying up output GTFs Open

frattalab/PAPA#37 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
'label' for novel transcripts reported by StringTie is hardcoded in get_combined_quant_gtf.py Open

low priority

frattalab/PAPA#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
get_combined_quant_gtf.py - _ref suffix coordinates are for matching introns, should probably be removed Open

low priority

frattalab/PAPA#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Update code formatting for all scripts with black auto-formatter Open

low priority

frattalab/PAPA#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
update submit.sh to take config as command line argument & use conda prefix Open

frattalab/PAPA#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
add script to combine novel last exons into single GTF to repo Open

frattalab/PAPA#46 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
NameError - name 'CONTRAST_NAME' is not defined if run_differential set to False Open

frattalab/PAPA#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
get_combined_quant_gtf - retain matching reference transcript ID from novel GTF Open

frattalab/PAPA#49 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
filter_tx_by_three_end - updating to atlas 3'end has unexpected(?) behaviour when polyA sites are intervals not single nucleotides Open

low priority

frattalab/PAPA#50 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Question about the novel_ref_combined.quant.last_exons.gtf Open

frattalab/PAPA#52 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
APA event type and ribosomes Open

frattalab/PAPA#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Environment dependency conflicts during pipeline setup Open

frattalab/PAPA#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

frattalab/PAPA

Get new issues in your inbox