I haven’t worked with hybrid genome before, I am trying to create a custom genome to align RNA-Seq that was generated from hybrid mouse. Would you please guide me how to create a custom genome for two hybrid mouse? The strains are C57BL and 6NJ. I have aligned to the mouse reference genome (C57BL) and the unique aligned reads percentage is around 65%, this is not good from my experience.
You can directly download the FASTA sequences from C57BL_6NJ_v1 assembly for Mus musculus from here under "Chromosome" tab. After downloading, you can concatenate all the FASTA files into one to generate a reference fasta for alignment of RNA-seq reads. You can use below code for creating single reference fasta:
cat fasta_file1 fasta_file2 fasta_filen > reference fasta