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frattalab

6 indexed repositories · View on GitHub

splicing
Snakemake pipeline for running MAJIQ

R · 23 stars
rna_seq_snakemake
Snakemake Pipeline For RNA-Seq in UCL Cluster

Python · 10 stars
PAPA
PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data

Python · 2 stars
QAPA_snakemake
Snakemake pipeline to run QAPA and perform differential polyA site usage analysis

Python · 1 star
rna_seq_single_steps
Snakemake pipelines for common bioinformatics tasks

Python · 0 stars
cryptic_biology
Analysis code for the cryptic biology paper

HTML · 0 stars

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TODO - make conda environments for each rule Open

frattalab/splicing#11 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
TODO - Update the config to take the PSI cutoffs for cryptic exons Open

good first issue

frattalab/splicing#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
DEXSeq & _PAR_Y genes - paralogues are grouped with counterparts for differential usage analysis Open

frattalab/QAPA_snakemake#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
feat: Calculate average & delta PAUs for provided contrasts Open

enhancement

frattalab/QAPA_snakemake#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
feat: Add average & delta PAU values to final 'processed' DEXSeq results table Open

frattalab/QAPA_snakemake#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
submit.sh for UCL/sge cluster - add an extra positional argument for --singularity-prefix Open

frattalab/QAPA_snakemake#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
chore: use_precomputed_bed needs to be set to True to use 'metadata_txt' path, otherwise redundant make_identifiers_tbl rule is triggered Open

frattalab/QAPA_snakemake#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
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
Some submit scripts do not use the conda environment Open

bug

frattalab/rna_seq_single_steps#3 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Definition of junction categories in compendium_cryptics Open

frattalab/cryptic_biology#3 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Make schema for sample_table.csv to try and catch layout errors Open

enhancement low priority

frattalab/rna_seq_snakemake#8 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Option to create (strand-specific) coverage bigwigs Open

enhancement low priority

frattalab/rna_seq_snakemake#14 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Test data bundled with repo to cover all permutations Open

frattalab/rna_seq_snakemake#27 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Move to snakemake profiles for cluster submission and job logs to main output dir not submissions Open

low priority

frattalab/rna_seq_snakemake#30 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Refine minimal QC modules and reporting Open

frattalab/rna_seq_snakemake#38 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
use of conda has us approaching file limits Open

frattalab/rna_seq_snakemake#55 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
DESEQ2 snakemake rule runs every comparison in the comparisons.yaml everytime it runs Open

frattalab/rna_seq_snakemake#56 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
conda instead of mamba Open

frattalab/rna_seq_snakemake#57 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

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