Hybrid ScRNA Seq genome (transcriptome

Question

[Kay]

Single-cell transcriptome alignment and read count estimation The droplet-based sequencing reads were aligned to the hybrid human genome hg38 and P. falciparum pd37 (PlasmoDB-46_Pfalciparum3D7_Genome.fasta) to remove any human transcript contamination. This was achieved using CellRanger v5.0.1 standard pipeline using --nosecondary flag. The raw gene count matrix was subjected to various single-cell pre-processing steps separately.

I saw tihis article that created a hybrid reference human and Plasmodium transcriptome for cell ranger Scrna analysis. I am wondering how i can make a similar reference genome.

Can anyone guide me in the right direction?

Thank you.

[dsull]

Can't you just concatenate the two FASTA files and the two GTF files together? (If the two species have the same chromosome names, then just rename the chromosomes in your FASTA file and GTF file for P. falciparum)