Hello to all,

I have a question about salmon and more precisely the alignment part. I use salmon on BAM files of RNAseq data and the problem is that I don't really know what to use as <LIBTYPE>.

I used -l A to get the automatic library but the "meta_info.json" it gives me:

 "salmon_version": "1.4.0",
    "samp_type": "none",
    "opt_type": "vb",
    "quant_errors": [],
    "num_libraries": 1,
    "library_types": [
        "MU"
    ],

"MU" but what puzzles me is that my datas are IlluminaTruSeq Stranded. "MU" is used for unstranded then it's a little weird....

I tested every libraries and MU gives me the better percentage with 60% of mapping, the other ISF, IU, ISR give less than 10-20% maximum

Is there a problem to use MU on stranded knowing that it is salmon who chose automatically ? Especially since this is what gives me the best results...

Thanks for your help

Aka