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13 Open 28 Closed
13 Open 28 Closed
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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! What’s not been updated in a month: updated:<2024-11-29.