Skip to content

Issues: frattalab/PAPA

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

13 Open 28 Closed
13 Open 28 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

filter_tx_by_three_end - updating to atlas 3'end has unexpected(?) behaviour when polyA sites are intervals not single nucleotides low priority
#50 opened Jul 4, 2023 by SamBryce-Smith
get_combined_quant_gtf - retain matching reference transcript ID from novel GTF
#49 opened Jun 20, 2023 by SamBryce-Smith
NameError - name 'CONTRAST_NAME' is not defined if run_differential set to False
#48 opened Apr 26, 2023 by SamBryce-Smith
add script to combine novel last exons into single GTF to repo
#46 opened Mar 30, 2023 by SamBryce-Smith
update submit.sh to take config as command line argument & use conda prefix
#45 opened Mar 30, 2023 by SamBryce-Smith
Update code formatting for all scripts with black auto-formatter low priority
#42 opened Jan 3, 2023 by SamBryce-Smith
get_combined_quant_gtf.py - _ref suffix coordinates are for matching introns, should probably be removed low priority
#41 opened Jan 3, 2023 by SamBryce-Smith
'label' for novel transcripts reported by StringTie is hardcoded in get_combined_quant_gtf.py low priority
#40 opened Nov 30, 2022 by SamBryce-Smith
Meta-issue - tidying up output GTFs
#37 opened Oct 13, 2022 by SamBryce-Smith
Intronic/'upstream' last exons - expand quantification regions to upstream penultimate exon/ shared region & add decoy transcripts enhancement New feature or request high priority This should be worked asap
#36 opened Oct 13, 2022 by SamBryce-Smith
1
Remove/collapse duplicate transcripts from combined quantification GTF low priority
#34 opened Oct 13, 2022 by SamBryce-Smith
Check that number of event log messages count up excluding duplicates low priority
#14 opened Sep 7, 2021 by SamBryce-Smith
sge profile not working for UCL SGE cluster bug Something isn't working
#4 opened Jul 30, 2021 by SamBryce-Smith
ProTip! Type g i on any issue or pull request to go back to the issue listing page.