frattalab PAPA issues - Githubissues

frattalab / PAPA

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

GNU General Public License v3.0

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filter_tx_by_three_end - updating to atlas 3'end has unexpected(?) behaviour when polyA sites are intervals not single nucleotides

#50 SamBryce-Smith opened 1 year ago
0
get_combined_quant_gtf - retain matching reference transcript ID from novel GTF

#49 SamBryce-Smith opened 1 year ago
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NameError - name 'CONTRAST_NAME' is not defined if run_differential set to False

#48 SamBryce-Smith opened 1 year ago
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Replace SatuRn with DEXSeq

#47 SamBryce-Smith closed 1 year ago
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add script to combine novel last exons into single GTF to repo

#46 SamBryce-Smith opened 1 year ago
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update submit.sh to take config as command line argument & use conda prefix

#45 SamBryce-Smith opened 1 year ago
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bug: run_differential_usage.R - undefined columns selected with rowMeans

#44 SamBryce-Smith closed 1 year ago
1
Optionally pass additional command line flags to Salmon quant

#43 SamBryce-Smith closed 1 year ago
1
Update code formatting for all scripts with black auto-formatter

#42 SamBryce-Smith opened 1 year ago
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get_combined_quant_gtf.py - _ref suffix coordinates are for matching introns, should probably be removed

#41 SamBryce-Smith opened 1 year ago
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'label' for novel transcripts reported by StringTie is hardcoded in get_combined_quant_gtf.py

#40 SamBryce-Smith opened 1 year ago
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v0.2.0

#39 SamBryce-Smith closed 6 months ago
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[Meta] - v0.2.0

#38 SamBryce-Smith closed 6 months ago
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Meta-issue - tidying up output GTFs

#37 SamBryce-Smith opened 1 year ago
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Intronic/'upstream' last exons - expand quantification regions to upstream penultimate exon/ shared region & add decoy transcripts

#36 SamBryce-Smith opened 1 year ago
1
get_combined_quant_gtf.py - annotate 'event types' for reference last exons

#35 SamBryce-Smith closed 1 year ago
1
Remove/collapse duplicate transcripts from combined quantification GTF

#34 SamBryce-Smith opened 1 year ago
0
Add synthetic test data than can package with repo

#33 SamBryce-Smith closed 1 year ago
2
Deprecate ability to provide multiple StringTie parameter options/combinations

#32 SamBryce-Smith closed 1 year ago
1
Hook up differential usage script to pipeline

#31 SamBryce-Smith closed 1 year ago
1
Make sure gene_name is propagated throughout novel last exons GTFs

#30 SamBryce-Smith closed 1 year ago
2
Script to filter GTF file based on attributes

#29 SamBryce-Smith closed 2 years ago
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Code to sum expression by pA site, doc updates, various other changes

#28 SamBryce-Smith closed 2 years ago
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output matrix of polyA isoform TPMs

#27 SamBryce-Smith closed 2 years ago
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Generate 'final' match_stats.tsv file combining filtering scripts and tracking transcript IDs across scripts

#26 SamBryce-Smith closed 1 year ago
1
Update filtering plumbing

#25 SamBryce-Smith closed 2 years ago
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Script to assign transcript isoforms to shared poly(A) sites (and last exons)

#24 SamBryce-Smith closed 2 years ago
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Add script to filter transcripts by min mean TPM by condition (filter_tx_by_condition_tpm.py)

#23 SamBryce-Smith closed 2 years ago
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Add script to filter transcripts based on presence of 3'end nearby Atlas polyA sites or conserved PAS motifs

#22 SamBryce-Smith closed 2 years ago
1
filter_tx_by_pas.py - add script to filter transcripts for last exons with nearby PolyASite sites or PAS motifs

#21 SamBryce-Smith closed 2 years ago
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Add minimum extension length filter to filter_tx_by_intron_chain.py

#20 SamBryce-Smith closed 2 years ago
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filter_tx_by_intron_chain.py - add minimum length filters for extension events

#19 SamBryce-Smith closed 2 years ago
0
filter_tx_by_intron_chain.py - 'internal_intron_spliced' events likely excludes events in the final reference intron

#18 SamBryce-Smith closed 1 year ago
1
filter_tx_by_intron_chain.py - reference annotation source can be 'none' so no filtering for gene type is performed

#17 SamBryce-Smith closed 1 year ago
1
filter_tx_by_intron_chain.py - add checks for empty dataframes when doing gr.apply / gr.assign to avoid KeyErrors & needing df conversion

#16 SamBryce-Smith closed 2 years ago
2
filter_tx_by_intron_chain.py - Only change exon_number to int once, then get_* functions just do a type check

#15 SamBryce-Smith closed 1 year ago
1
Check that number of event log messages count up excluding duplicates

#14 SamBryce-Smith opened 2 years ago
0
Move to paramspace and wrapper script to call stringtie with different parameter combos

#13 SamBryce-Smith closed 1 year ago
1
filter_tx_by_intron_chain.py - get_terminal_regions uses sort & .duplicated(subset="transcript_id", keep=<first/last>)

#12 SamBryce-Smith closed 2 years ago
1
filter_tx_by_chain.py - use .duplicated(subset="transcript_id", keep=False) to remove single_exon transcripts

#11 SamBryce-Smith closed 2 years ago
1
filter_tx_by_intron_chain.py - get_internal_exons could avoid groupby using sort + ~ duplicated(keep="last")

#10 SamBryce-Smith closed 2 years ago
1
filter_tx_by_intron_chain.py - Consider groupby.rank() for adding intron_numbers by transcript

#9 SamBryce-Smith closed 2 years ago
1
filter_tx_by_intron_chain.py - annotate 'isoform class' for all event types (intronic_spliced, ds_spliced, 3'UTR introns etc.)

#8 SamBryce-Smith closed 2 years ago
2
filter_tx_by_intron_chain.py - refactor functions to take first/last introns etc. as input to prevent being generated multiple times

#7 SamBryce-Smith closed 1 year ago
1
Replace assembled first exons of matched novel transcripts with matching reference first exon

#6 SamBryce-Smith closed 1 year ago
1
filter_by_tx_chain.py - add code to extract first intron novel last exons with exact match at 3'end boundary of ref first exon

#5 SamBryce-Smith closed 2 years ago
1
sge profile not working for UCL SGE cluster

#4 SamBryce-Smith opened 2 years ago
0
filter_by_tx_chain.py - refactor implementation of match_by="transcript"

#3 SamBryce-Smith closed 1 year ago
1
Support for Ensembl style GTF files

#2 SamBryce-Smith closed 2 years ago
1
filter_by_tx_chain.py - use sort_introns_by_strand via pyranges.apply for multiprocessing speed up

#1 SamBryce-Smith closed 2 years ago
1