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!!
Beware of endogenous elements in your artificial contigs. If reads map to multiple locations they will be dropped. Consider this with the coverage bias specific to 5' or 3' kit.
As mentioned ^^, 10x GEX data is a reduced representation. Without proper sequencing depth :: sequencing saturation detection can limited.