Place to put the script I used to pre-process scRNA-seq CCRCC sample data before running inferCNV for A1 and integrated(A1,B2 and D2)
- h5 file for the scRNA-seq data (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices). Ensambl gene id and symbol mapping extracted from this file.
- Seurat Object after QC and ready to be analyzed saved as .rds file
- Genome position file. Can use the one in this repo "gencode_v19_gen_pos_sym_only.txt" or can be downloaded from TrinityCTAT https://data.broadinstitute.org/Trinity/CTAT/cnv/
Aug. 21 2019 CMo