Using salmon v0.82 on Debian Linux cluster, I tried the following quant command:
salmon quant -i mouseRNA_index -l -r ./fastq/S1_R1.fastq.gz -p 8 -o quants/S1_R1_quant
but obtained a libType error:
Version Info: This is the most recent version of Salmon. Exception : [the option '--libType' is required but missing]. Exiting.
Having read the Salmon documentation, I thought that the above syntax should describe my unstranded single-end read library, but I get the '
--libType' is required but missing' error message. I tried different variants without success. Can someone explain the problem with my syntax please?