Create custom references for Macaca fascicularis using Cellranger -arc

Question

[tranhangk15cnsh]

I conducted the single nuclei RNA sequencing and single nuclei ATAC sequencing for Macaca fascicularis. Now I need to create a custom reference for mapping. I plan to use the the genome from the Ensembl: https://asia.ensembl.org/Macaca_fascicularis/Info/Index However, there are many fasta files and and one gtf file, so there are errors when I tried to run the cellranger-arc mkref. I think that I need to split the gtf file so each gtf file only contains the config name for the corresponding fasta files, but I am not sure my thinking is correct or not. So I want to ask everyone here to make sure I am on the right track.

Thank you so much for your help!!!

Answer 1

[GenoMax]

Use the following files:

genome: https://ftp.ensembl.org/pub/release-113/fasta/macaca_fascicularis/dna/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz
gtf: https://ftp.ensembl.org/pub/release-113/gtf/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_6.0.113.gtf.gz

toplevel file contains multi fasta sequence from all chromosomes.This file is equivalent to primary assembly file. See README for more information: https://ftp.ensembl.org/pub/release-113/fasta/macaca_fascicularis/dna/README

[tranhangk15cnsh]

Oh thank you so much!!!!