Preview

bartongroup-two_pass_alignment_pipeline-225ac87
- .gitignore
  
  2.3 kB
- .gitmodules
  
  99 Bytes
- 2passpipeline.yml
  
  115 Bytes
- README.md
  
  2.7 kB
- annotations
  - arabidopsis
    - fetch_annotations.sh
      
      765 Bytes
  - human
    - fetch_annotations.sh
      
      730 Bytes
  - mouse
    - fetch_annotations.sh
      
      715 Bytes
  - yeast
    - fetch_annotations.sh
      
      818 Bytes
- images
  - rulegraph.png
    
    328.6 kB
  - rulegraph.svg
    
    12.9 kB
  - rulegraph_sim.png
    
    748.5 kB
  - rulegraph_sim.svg
    
    21.4 kB
- notebooks
  - benchmark_two_pass_alignment.ipynb
    
    390.6 kB
  - benchmark_two_pass_transcript_assembly.ipynb
    
    492.6 kB
  - decision_trees.ipynb
    
    944.3 kB
  - figures
    - arabidopsis_decision_tree_1_confusion_matrix.svg
      
      5.2 kB
    - arabidopsis_decision_tree_2_confusion_matrix.svg
      
      5.2 kB
    - arabidopsis_drs_stringtie_benchmark.svg
      
      24.2 kB
    - arabidopsis_isoseq_stringtie_benchmark.svg
      
      21.0 kB
    - arabidopsis_lr_donor_score_confusion_matrix.svg
      
      5.5 kB
    - arabidopsis_lr_scores_confusion_matrix.svg
      
      16.1 kB
    - arath_junc_decision_tree_1_final.svg
      
      46.0 kB
    - arath_junc_decision_tree_2_final.svg
      
      64.3 kB
    - correct_percentage_filtered_2pass.svg
      
      33.5 kB
    - correct_percentage_flair.svg
      
      26.4 kB
    - correct_percentage_naive_2pass.svg
      
      26.5 kB
    - feature_importances.svg
      
      7.7 kB
    - human_cdna_stringtie_benchmark.svg
      
      23.3 kB
    - human_decision_tree_1_confusion_matrix.svg
      
      5.2 kB
    - human_decision_tree_2_confusion_matrix.svg
      
      5.2 kB
    - human_drs_stringtie_benchmark.svg
      
      25.7 kB
    - human_isoseq_stringtie_benchmark.svg
      
      26.2 kB
    - incorrect_percentage_filtered_2pass.svg
      
      55.9 kB
    - incorrect_percentage_flair.svg
      
      44.1 kB
    - individual_metric_confusion_matrices.svg
      
      19.2 kB
    - jad_annot_vs_unannot.svg
      
      11.7 kB
    - mouse_cdna_stringtie_benchmark.svg
      
      21.7 kB
    - mouse_drs_stringtie_benchmark.svg
      
      22.2 kB
    - primary_donor_acceptor_metric_confusion_matrices.svg
      
      10.0 kB
    - quantification_spearmanr_filtered_2pass.svg
      
      32.1 kB
    - sequence_lr_model_diagram.svg
      
      52.0 kB
    - simulated_data_identity.svg
      
      18.5 kB
    - simulated_data_indels.svg
      
      21.2 kB
    - simulated_data_mismatches.svg
      
      21.6 kB
    - simulated_data_stringtie_benchmark.svg
      
      23.9 kB
    - two_pass_method.svg
      
      102.6 kB
    - yeast_drs_stringtie_benchmark.svg
      
      26.0 kB
  - figures_final
    - figure1.png
      
      290.7 kB
    - figure1.svg
      
      3.7 MB
    - figure2.png
      
      341.9 kB
    - figure2.svg
      
      685.8 kB
    - figure3.png
      
      594.2 kB
    - figure3.svg
      
      307.6 kB
    - figure4.png
      
      693.1 kB
    - figure4.svg
      
      140.4 kB
    - figure5.png
      
      417.5 kB
    - figure5.svg
      
      155.1 kB
    - figure6.png
      
      989.2 kB
    - figure6.svg
      
      307.6 kB
    - suppfigure1.png
      
      265.0 kB
    - suppfigure1.svg
      
      202.0 kB
    - suppfigure2.png
      
      327.2 kB
    - suppfigure2.svg
      
      207.3 kB
    - suppfigure3.png
      
      199.4 kB
    - suppfigure3.svg
      
      38.9 kB
    - suppfigure4.png
      
      181.7 kB
    - suppfigure4.svg
      
      30.5 kB
    - suppfigure5.png
      
      518.4 kB
    - suppfigure5.svg
      
      673.6 kB
    - suppfigure6.png
      
      858.4 kB
    - suppfigure6.svg
      
      212.4 kB
  - flm_example_figures.ipynb
    
    13.7 kB
  - read_simulation.ipynb
    
    115.2 kB
- pipeline
  - Snakefile
    
    1.4 kB
  - arabidopsis_drs
    - config.yml
      
      1.9 kB
    - fetch_data.sh
      
      3.7 kB
  - arabidopsis_isoseq
    - config.yml
      
      1.5 kB
  - human_cdna
    - config.yml
      
      1.9 kB
  - human_drs
    - config.yml
      
      1.9 kB
    - fetch_data.sh
      
      1.9 kB
  - human_isoseq
    - config.yml
      
      2.1 kB
  - mouse_cdna
    - config.yml
      
      1.6 kB
  - mouse_drs
    - config.yml
      
      1.6 kB
  - yeast_drs
    - config.yml
      
      1.8 kB
- rules
  - 2passtools.snakefile
    
    3.2 kB
  - assembly.snakefile
    
    991 Bytes
  - benchmarking.snakefile
    
    1.2 kB
  - env_yamls
    - 2passtools.yml
      
      252 Bytes
    - bedtools.yml
      
      84 Bytes
    - flair.yml
      
      124 Bytes
    - minimap2.yml
      
      99 Bytes
    - stringtie.yml
      
      106 Bytes
    - yanosim.yml
      
      198 Bytes
  - flair.snakefile
    
    838 Bytes
  - input.snakefile
    
    2.6 kB
  - minimap2.snakefile
    
    3.2 kB
  - simulation.snakefile
    
    2.1 kB
- scripts
  - get_sim_counts_from_reads.py
    
    1.4 kB
  - minimap2
  - score_simulated.py
    
    5.1 kB

bartongroup/two_pass_alignment_pipeline-v0.1.zip