I have 3 reference genomes and I wish to align my FASTQ reads against all 3 of them. I have used
hisat2-build to build individual indexes of all 3 of them, but couldn't find the command to make an index of multiple genomes.
I have run the following command for alignment -
hisat2 -p 4 individual_index --dta --rna-strandness RF -1 paired_1.fastq -2 paired_2.fastq -S aligned.sam
I want to run alignment with all 3 indexes in one go with HISAT2. Also, I cannot use STAR as I am using an 8 gig ram system.