Quick questions about Alevin and AlevinQC

I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation

  1. How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin.

  2. The alevin_meta_info.json says Number of mapped reads. Are these Uniquely+multimappig reads or just Uniquely mapping reads.

  3. For all of my samples the library type couldn’t be determined. I got the following log for example. I used ISR since the data was generated from Chromium 3′ V3 chemistry.
"expected_format": "ISR",
    "compatible_fragment_ratio": 1.0,
    "num_compatible_fragments": 11147644,
    "num_assigned_fragments": 11147644,
    "num_frags_with_concordant_consistent_mappings": 0,
    "num_frags_with_inconsistent_or_orphan_mappings": 15681780,
    "strand_mapping_bias": 0.0,
    "MSF": 0,
    "OSF": 0,
    "ISF": 0,
    "MSR": 0,
    "OSR": 0,
    "ISR": 0,
    "SF": 0,
    "SR": 0,
    "MU": 0,
    "OU": 0,
    "IU": 0,
    "U": 0
  1. When I run AlevinQC why the Number of used reads (which Alevin documentation says are reads that are used for quantification) greater than Number of mapped reads.
    alevinqc

I am using the following command

~/salmon-1.5.2_linux_x86_64/bin/salmon alevin -l ISR -1 R1_001.fastq.gz -2 R2_001.fastq.gz --chromiumV3 --dumpFeatures --dumpMtx --expectCells 200 -i salmon_index/ -p 20 -o sample1 --keepCBFraction 1 --numCellBootstraps 100 --tgMap tx2gene.txt &
  1. When I set --keepCBFraction 1, does setting --expectCells 200 make sense. I am asking this because I didn’t see any change in mapping percentages of reads and cell barcodes being thrown out when I use both.

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