I add here my question, because it is about both GRCm38 and mm10 reference genomes.
I have received the fastq files of some Bisulfite sequencing samples. For the sequencing they have used "gem3.mmusculus.GRCm38_BS" as a reference. But I am not sure what genome to use for the analysis (the alingment). I think the correct one will be the GRCm38, but I have other older RNA sequences anayzed with the mm10 reference genome, and I would like to compare both of them in the future.
Is it posible to compare some sequences with the GRC38 genome and others with the mm10 genome, for example at the UCSC genome browser (with the bedgraph files I mean)?
Is there a way to change something in the fastq files of the bisulfite sequencing for example to finally do the alignment with the mm10 reference genome?