Create customized gene annotation file

Question

[rhonddaskl]

Hi,

I have self-defined RNA sequence, it was used to tag the special cells I'm interested in. I want to use cellranger mkref to build a custom reference and use this reference file to count the cells that have this sequence. Do you have any ideas on how to generate gtf/fasta files if I only have an RNA sequence?

Thanks!!!

Answer 1

[ATpoint]

Plese confirm whether you read and tried the manual: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#marker

[rhonddaskl]

Thanks!! This is exactly what I need!