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Confusion about Salmon library type

I am not so sure about my library type but I chose IU in my Salmon analysis:

salmon quant -i BANY_transcript_index -p 36 --libType IU -g salmon/BANY_v2.gtf -1 ${i}_1P.fq.gz -2 ${i}_2P.fq.gz --validateMappings -o ${i}.quant

Got a message in the log:

Detected a *potential* strand bias > 1% in an unstranded protocol check the file: /media/nus/AMLab_Ext1/Shen/salmon/DS_1_HW_FM.quant/lib_format_counts.json for details

The mapping rate:

[2020-06-04 03:18:51.102] [jointLog] [info] Number of mappings discarded because of alignment score : 57,476,847
[2020-06-04 03:18:51.102] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,980,029
[2020-06-04 03:18:51.102] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-06-04 03:18:51.102] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 366,055
[2020-06-04 03:18:51.102] [jointLog] [info] Mapping rate = 62.376%

It shows that:

{
    "read_files": "[ DS_1_HW_FM_1P.fq.gz, DS_1_HW_FM_2P.fq.gz]",
    "expected_format": "IU",
    "compatible_fragment_ratio": 1.0,
    "num_compatible_fragments": 20648911,
    "num_assigned_fragments": 20648911,
    "num_frags_with_concordant_consistent_mappings": 20405027,
    "num_frags_with_inconsistent_or_orphan_mappings": 1098322,
    "strand_mapping_bias": 0.12769010303196366,
    "MSF": 0,
    "OSF": 0,
    "ISF": 2605520,
    "MSR": 0,
    "OSR": 0,
    "ISR": 17799507,
    "SF": 539885,
    "SR": 558437,
    "MU": 0,
    "OU": 0,
    "IU": 0,
    "U": 0
}

Ok so what does it mean? Is IU an appropriate choice or should I go with ISR (automatically recognized when I assign -l A)? Based on my understanding, IU should cover both ISF and ISR right? then why IU is 0....I'm lost.

rna-seq alignment salmon next-gen genome
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written by tianshenbio tianshenbio

The library prep method tells you what to choose. Which kit was used?

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written by ATpoint ATpoint

That's performed by a sequencing company. They mentioned in the report:

First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

I think It should be unstranded...but I can clearly see strand bias (0.12) as Salmon reported...

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written by tianshenbio tianshenbio

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