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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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Cellranger mkref function parameters for Sierra #54

Open hkarakurt8742 opened 1 year ago

hkarakurt8742 commented 1 year ago

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 commented 1 year ago

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