Hello Biostars Community
I am newbie in bioinformatics field. We ran mice experiment using the CRE recombinant mice Cx3cr1tm2.1(cre/ERT2)Litt which we acquired from Jax laboratories (http://www.informatics.jax.org/allele/MGI:5450813). we did SmartSeq2 with 75bp on Illumina nextseq550 with four different treatment groups on the mice. Unfortunately the sequence of the mutation is not known, we enquired with the JAX laboratories and were further redirected to the donor of the mice from whom we are awaiting for the answer. Can someone suggest me how to create a custom reference genome with mm10 with the mentioned mutation in the above link so that I can do the mapping by STAR or any aligner and visualise the results of cre mice.
Thanks in advance
What exactly do you want to visualize? The knockout? From what I understand you have floxxed ERT2 so that gene should be deleted in your mice. I do not see why you would not want to use the standard mm10 reference genome. Please elaborate on the aim of your analysis.