Question: Understanding kallisto qc metrics in run_info.json
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gravatar for MutationalMeltdown
13 days ago by
MutationalMeltdown30 wrote:

I've ran kallisto bus on multiple read pairs (R1 and R2) fastq files (scRNA-seq 10x data) and I'm trying to understand the QC metrics in run_info.json:

    "n_targets": 0,
    "n_bootstraps": 0,
    "n_processed": 286634021,
    "n_pseudoaligned": 8387513897523690476,
    "n_unique": 50123568,
    "p_pseudoaligned": 2926210178492.3,
    "p_unique": 17.5,
    "kallisto_version": "0.46.0",
    "index_version": 0,

I read here what the metrics mean: http://pachterlab.github.io/kallisto//releases/2018/01/29/v0.44.0

However, for my data, p_pseudoaligned is >>100% and n_pseudoaligned >> n_processed. What I expected was that p_pseudoaligned would be somewhat analagous to % read alignment/mapping with a 'normal' aligner. What am I missing? Thank you

EDIT: posted to forum

ADD COMMENTlink modified 10 days ago • written 13 days ago by MutationalMeltdown30

Please re-post at the Kallisto Google Group page, and kindly link back here (and vice-versa) - this will help the community: https://groups.google.com/forum/?nomobile=true#!forum/kallisto-sleuth-users

ADD REPLYlink modified 13 days ago • written 13 days ago by Kevin Blighe50k
1

I posted to the "kallisto-and-applications" forum

ADD REPLYlink written 10 days ago by MutationalMeltdown30
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