GENEVA

This is an analysis pipeline for GENEVA datasets. Please follow the following steps to execute your dataset.

• The dataset is composed of the gene expression of each single cell (coded by a Cell barcode).
• The same cell barcodes are connected to a HTO barcode (present in a different fastq file).
• Once you process the HTO fastq files, you use the cell barcodes to map the cells to their correct drug labels.
• Lastly, we perform the 3'end mRNA sequencing of cells to collect their genotype.
• We then use their genotype to map each cell BC to their corresponding cell line.

10x single-cell expression

1. Follow the script called cellranger_processing.sh in the scripts folder to convert fastq files into count matrices.
2. Follow the notebook called 10x_processing.ipynb in the notebooks folder to process your raw table into a processed matrix.

HTO Barcodes Demultiplexing (Cell-Hashing)

1. Follow the notebook called pymulti_processing.ipynb in the notebooks folder to process your HTO fastq files.
2. Follow the notebook called 10x_pymulti_merging.ipynb in the notebooks folder to merge your processed matrix with the demultiplexed data.

Cell-Line Genotype Demultiplexing

1. Follow the script called 3_end_mrna_processing.sh in the scripts folder to process all your mrna data into deduplicated bam files.

2. Follow the script called process_3_end_vcfs.sh in the scripts folder to process all your bam files into a final concatenated vcf file ready for demuxlet.

3. Follow the script called demuxlet_processing.sh in the scripts folder to process the merged vcf files along with the 10x outputs into a demultiplexed vcf files.

4. Follow the script called freemux_processing.sh in the scripts folder to process the demux outputs into clustered vcf outputs that sceasymode can analyze.

5. Follow the notebook called assign_genotypes_sceasymode.ipynb in the notebooks folder to process the final vcf files into dictionaries with the genotyping module of sceasy mode.

GENEVA Analyses

Follow the notebooks in the analysis_notebooks directory