Alignment for each sample against merged genomes, with STARsolo: arrayRunSTARSolo.sh.
This script calls runSTARSolo.sh for each sample.
It requires some preprocessing generating the genome index (genome_index.sh) and lists of fastq files to process (generate_fastq_lists.sh).
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, filter_fastqs.sh)
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.