I am trying to use sortmeRNA to know the details about the RNA present in my sample. I am using sortmeRNA for this. When I try to use it, it gives me an error saying: "'d' is not one of the options". Whereas, my command does not have "d" or spaces between them. Please let me know where I am going wrong.
The command which I used is:
sortmerna --ref /dir/ref.fa,/dir/SAindex --reads R1.fq R2.fq --aligned output.sortedByCoord.out.bam --match --coverage
Thanks for your help in advance