Hi,
I am also interested in using Arriba to find fusions for my single cell dataset since I could not find any reliable option for single cell data right now and in some benchmarking articles (here and here00058-4)) I have seen people used arriba on single cell data to benchmark with their method and it shows very faire and reliable outcomes. I am thinking of a workflow and am not sure if it makes sense to other people in the field as well, so I really appreciate your input and suggestions. so what I plan to do is: I have a single cell data sequenced with Illumina machine and aligned with cellranger algorithm, however, I am thinking of using arriba workflow which is using STAR, extract the fusion gene transcript from the expected and high confidence fusion genes and add them to my reference genome and use it on cellranger and realign and build my expression matrix this time containing fusion genes as well. Does this workflow make sense to you?
I appreciate your help, Sogi
