I have 3 genes that I need to add to the cellranger mouse reference genome database. I followed the "Add a Marker Gene to the FASTA and GTF" session in this tutorial:
The process was smoothly done and I can see the three genes have been added into the database (both in .fa file and in .gtf file of the reference genome database).
However, after cellranger count, I checked the genes that have been detected in our dataset, I don't see any of those genes (we are pretty sure they are supposed to be detected). So I'm wondering if there was step that I have missed so that the gene was not actually added?
Any suggestion would be very helpful!!
Thanks in advance!!