Recreating LongSom paper analysis - cbg-ethz/LongSom GitHub Wiki

LongSom paper results can be generated using the code in the paper_release tag. This release includes additional Snakemake workflows and Python scripts for QC, scWGS validation, etc. All data was generated using snakefiles/LongSom.smk, and figures were generated as follows.

Figure 2 was created using snakefiles/QC.smk, and specifically:

• 2a,b. QC/scripts/CellTypeReannotation/PlotCellTypeReannotation.py
• 2c,d. QC/scripts/CellTypeReannotation/PlotMutationalBurden.py
• 2e. QC/scripts/CellTypeReannotation/Clustermap.py

Figure 3 was created using snakefiles/QC.smk, and specifically:

• 3a. QC/scripts/Filters/Sankey.py
• 3b. QC/scripts/FunctionalAnno/FunctionalAnno.py
• 3c. QC/scripts/scDNAValidation/PlotWaffleChartscDNAValid.py
• 3d. QC/scripts/NoDistComparison/NoDistComparison.py

Empty droplets data for Figure 4 was created using QC/chrM_conta_valid/chrM_conta_valid.smk. Figure panels were created using QC/chrM_conta_valid/MitoContaFigures.ipynb

Figure 5 was created using snakefiles/QC.smk, and specifically:

• 5a,b. QC/scripts/ComparisonSComaticLongSom/ComparisonSComaticLongSom.py
• 5c,d. /ComparisonSComaticLongSom/PlotComparisonSComaticLongSom.py

Figure 6 was created using snakefiles/BnpC.smk

Figure 7 was generated using :

• 7a,c. QC/scripts/SRComparison/PlotSRComparison.py
• 7b. QC/scripts/FunctionalAnno/FunctionalAnno.py
• 7d. snakefiles/BnpC.smk