Preprocessing of Genotyping & scRna seq data

Checkpoint (1) 25/09/2023

Director: Pr. Lluis Quintana-Murci Co-supervisor: Dr. Maxime Rotival
Human Evolutionary Genetics Unit
Marwan Sharawy
Implementation of Established Pipeline (Single-cell eQTLGen Consortium)

• rerun the pipline to

solve issues with
libraries 82:88

• debugging doublet
IN PROGRESS
detection /scrublet
errors manually
• Working Group 1
(Genome imputation and
QC)

• Working Group 2 (Cell

Classification) pipeline
both of which will be
used for

• Working Group 3 (eQTL

Detection).

MGP van der Wijst. et, al. 2020

 Parallel implementaion of our own pipline

• Solved issues with genome lifting from hg19 to hg38 ( non lifting of 40% of all snps)

• Rerun Demuxlet for libraries 82:88

• Testing of 5 diffrent doublet detection methods

(scvi ,scrublet, doubletdetection, KNN>5 ‘Used in yan paper ‘ , KNN>10)

• Exclued scvi because of high run time and need for gpu
 KNN5

• Demuxlet identifies 11/12 of

doublets within a library
(doublets from different
individuals).

• Compare the undetected 1/12

doublets vs each doublet
detection method.

Conclusion : remove
• view PDF file for better
much more non
resolution
doublets than True
doublets
 Example of 1 library
adjusted accurcay : TrueDBLS/ method Total dbls * 12/11 to accuracy: method TrueDBLS/ method Total dbls
adjust for missed fraction of demuxlet power: method TrueDBLS/ Demuxlet True dbls

KNN5
61% accuracy DD
66% adjusted accuracy 76% accuracy
81% power of true doublets detection 83% adj-accuracy
77% power
11/12 True doublets KNN10
77% accuracy
84% adj-acc
65% power

1/12 expected doublets

 adjusted accurcay : TrueDBLS/ method Total dbls * 12/11 to
adjust for missed fraction of demuxlet

KNN5 Scrublet
61% accuracy DD 76% accuracy
66% adjusted accuracy 76% accuracy 0.82 adj-accuracy
81% power of true doublets detection 83% adj-acc 75% power
77% power

KNN10
77% accuracy
84% adj-acc
65% power
Example of 1 library

DD&knn10 &scr
accuracy 89%
power 55%
DD&scr
DD&KNN5 accuracy 0.81% DD&knn5&scr
accuracy 84% power %75 accuracy85 %
power 66% power %66
DD&knn10
accuracy 88%
power 59%
KNN10

Conclustion : same as KNN5

remove more cells than The

expected doublet rate
Combining KNN10 & DD

Conclustion :
most responable
doublet detected rate
using the combination
of KNN10 +
Doubletdetection tool
EXAM ON 15TH OF NOVEMBER
spend 11: 14 november studying
 To Do

• Continuing scRna processing: Utilizing the best methods after assessing various
tools for doublet detection, Further QC as removing dead cells ( high % mt and
low count reads per cell ), automatic cell labeling

• Implementing stage 2 of the consortium pipeline after fixing errors of part 2.

• October 23-27: Mandatory Hub for R& Statistic Course designed for Ph.D.
students.
KNN5 Scrublet
0.56% accuracy DD 71% accuracy
61% adjusted accuracy 75% accuracy 0.77adj-accuracy
81% power of true doublets detection 83% adj-acc 0.54% power
43% power

KNN10
67% accuracy
73% adj-acc
69% power
0.83 0.87
0.86 0.79

84% acc