Understanding kallisto qc metrics in run_info.json
0
0
Entering edit mode
20 months ago

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

RNA-Seq kallisto scRNA-seq alignment • 1.2k views
ADD COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2576 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6