• Alignment for each sample against merged genomes, with STARsolo:

    This script calls for each sample.

    It requires some preprocessing generating the genome index ( and lists of fastq files to process (

    The genomes were download already merged from 10x.

  • Classify cell barcodes by specie, separate_barcodes.R

  • Filter the fastq files, separating the reads according by the classification of their barcode (human or mouse)(in process,

  • Realign the human and mouse fastq files with their respective genome, so all reads from a same cell are uniformly aligned to the same genome.