Viktor Petukhov PRO
PhD student at the University of Copenhagen
Introduction
*http://thescienceexplorer.com/brain-and-body/fat-tissue-shields-cancer-cells-chemo-study-finds
**https://support.10xgenomics.com/single-cell-gene-expression/instrument/doc/user-guide-chromium-single-cell-controller-readiness-test
Fastq files
with
barcoded
reads
(CB + UMI)
**
Single cells
Sequencing
*
Barcoding system
Barcoding system
Barcoding system
Cell barcode errors
Gene 1
Gene 2
Gene 3
UMI 3: x15
UMI 2: x1
UMI 1: x3
UMI 4: x2
UMI 4: x1
UMI 5: x3
AAAATTTGGG
Gene 1
Gene 2
Gene 3
UMI 3: x5
UMI 1: x1
UMI 5: x1
AAAACTTGGG
Gene 1
Gene 2
Gene 3
UMI 3: x10
UMI 2: x1
UMI 1: x2
UMI 4: x2
UMI 4: x1
UMI 5: x2
AAAATTTGGG
UMI collisions
UMI N
...
UMI 6
UMI 5
UMI 4
UMI 3
UMI 2
UMI 1
UMI pool:
UMI 4
UMI 7
UMI 1
Gene 1
UMI 4
UMI 7
UMI 1
: x10
: x3
: x15
28 reads; 3 UMIs
Expression level: 3
Cell 1
UMI 5
Gene 1
UMI 4
UMI 7
UMI 1
UMI 3
UMI 9
UMI 9
: x1
: x2
: x8
UMI 2
: x4
Cell 2
28 reads; 3 UMIs
Expression level: 3
UMI 2
Gene 1
UMI 3
UMI 9
: x1
: x10
: x4
Cell 2
UMI errors
Gene 1
Gene 1
UMI 3: x15
UMI 2: x1
UMI 1: x3
UMI 3: x9
UMI 1: x5
GTTA: x15
GGAC: x1
AATT: x3
UMI 4: x3
UMI 5: x1
GTTA: x9
AATT: x5
AGAG: x3
GTAA: x1
GTAA: x1
Cell 1
Cell 2
Expression
level: 3
Expression
level: 4
Real expression
level: 3
Real expression
level: 3
UMI errors. Simple approach
GTTA: x13
TGAC: x1
AATT: x3
GGAC: x1
GGTA: x8
GTCA: x4
GCCA: x2
GTTT: x15
Total number of molecules: 8
UMI errors
GTTA: x13
TGAC: x1
AATT: x3
GGAC: x1
GGTA: x8
GTCA: x4
GCCA: x2
GTTT: x15
Total number of molecules: 3
Bordaeux, demultiplexing
By Viktor Petukhov
