Hi! I am trying to run RNA quantification through the salmon program (I am using version 1.2.1), using the pre-computed salmon index downloaded from refgenie (link can be found here). I am having a bit of trouble with the options in the command line and keep receiving error messages.
Here is the command I am passing through:
salmon quant -i <directory containing index> -l A -1 <(gzip <path to .fastq.gz file>) -2 <(gzip <path to .fastq.gz file>) --validateMappings -o <output directory>
Here is what
directory containing the index has in it. I am passing the directory's path into the
I downloaded this entire folder from the refgenie link provided above.
Here is what the error message looks like.