We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells.
<details><summary>Code</summary>
`python disambiguate.py -a bwa -s Sample_10_395_3 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam`
</details>
`python disambiguate.py -a bwa -s SampleID 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam`