Salmon libType is required but missing, although I thought I supplied it

Question

[charlesmagnefr]

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? Thanks, Charles.

[charlesmagnefr]

Yes Rob, that worked. Thank you for the quick response! Charles

[WouterDeCoster]

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Answer 1

[Rob]

Hi Charles,

The issue is that the libtype flag -l (short form) or --libType (long form) requires an argument. In your case, this would be U for unstranded. So, your full command would look like:

cm@node10:~/mouseRNAseq$ salmon quant -i mouseRNA_index -l U -r ./fastq/S1_R1.fastq.gz -p 8 -o quants/S1_R1_quant

let me know if this works.

--Rob