Cellranger mkref function parameters for Sierra

[hkarakurt8742]

Hello,
I am using 10X datasets with Cellranger and I want to use Sierra for AS analysis. I am using Ensembl GRCh38 genome and GTF files and I build my own reference. I used the tutorial from 10X Website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr). I used this code to prepare GTF file:

cellranger mkgtf my_gtf.gtf my_gtf.filtered.gtf --attribute=gene_biotype:protein_coding

Does "--attribute" parameter effects the performance or sensitivity of Sierra?

Thank you in advance.

[rj-patrick]

Hi @hkarakurt8742,

The attribute parameter here will just be filtering the GTF file for protein coding genes so that will be fine for Sierra,

Cheers,
Ralph