Comments (3)
huangyh09
commented on August 11, 2024
Hi, the briekit-event-filter is only for the skipping exon events. You may need to define your own filters for the A3SS (alternative 3' splice site) event, which we haven't looked into.
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Ivymanman
commented on August 11, 2024
Thanks a lot π
εθͺζηiPhone------------------ Original ------------------From: Yuanhua Huang <[email protected]>Date: Sat,Aug 3,2019 4:57 PMTo: huangyh09/briekit <[email protected]>Cc: Ivymanman <[email protected]>, Author <[email protected]>Subject: Re: [huangyh09/briekit] briekit-event-filter (#1)Hi, the briekit-event-filter is only for the skipping exon events. You may need to define your own filters for the A3SS (alternative 3' splice site) event, which we haven't looked into.
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jihongma1010
commented on August 11, 2024
hi, I got this error when I run
briekit-event -a /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf -o /disk2/brie_rnasplicing_bc25/bc25_as/
Making GFF alternative events annotation...
- Input annotation files: /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf
- Output dir: /disk2/brie_rnasplicing_bc25/bc25_as/
('Reading table', '/disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf')
Traceback (most recent call last):
File "/home/JHma/miniconda3/envs/RNASEQ/bin/briekit-event", line 11, in
load_entry_point('briekit==0.2.2', 'console_scripts', 'briekit-event')()
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 175, in main
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 69, in defineAllSplicing
File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 39, in prepareSplicegraph
File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 85, in populateSplicegraph
File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 64, in readTable_gff
UnboundLocalError: local variable 'exons' referenced before assignment
Could you help me? Thanks
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Related Issues (8)
- briekit-event error: UnboundLocalError: local variable 'exons' referenced before assignment HOT 1
- Problem when filtering splicing event with ENSEMBL GTF file. HOT 1
- About using brisket on other species HOT 2
- Missing posterior plots in sashimi plot HOT 5
- Briekit-events output fewer genes than expected HOT 2
- briekit with ensembl gtf HOT 1
- parseTables Error HOT 2
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