making a customer reference by using cell ranger Anyone here knows how to add a new gene (GFP) to customer reference by using cellranger? We use the Cre/loxp system by using R26RmTmG mice and want to use GFP to isolate specific cells. I have read the cellranger workflow but still, have no idea how to do it. Like it is said that I should update the GTF file as shown in the screenshot.
Step 1: 
Add the the GFP sequence to your fasta file

&gt;GFP_name
ATG.....TAA


Step 2:
Annotate the gtf so that it contains all the necessary information to annotate your information

Add this line to your GTF file but modify where necessary:
"Make sure that all columns are tab separated"

GFP_name    AddedGene   exon    1   1966    .   +   1   gene_id "GFP"; transcript_id "GFP"; gene_name "GFP"; transcript_name "GFP"



The first column has to correspond to the header of the fasta sequence 
start and end indicates the length of your sequence. I added a 1966 bp long sequence to my gtf


Code example:
step 1:

cat reference.fa gfp_seq.fa &gt; new_reference.fa


step 2:

cat genes.gtf gfp.gtf &gt; new_genes.gtf


-  gfp_seq.fa is your custom gene in fasta file
-  gfp.gtf is your custom gtf line or lines if you want to add more

You can also open your current reference fasta and gtf file in a text editor and copy paste the sequence and gtf line in there. 

Then run cellranger mkref on your new_reference and new_genes file