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

Bordaeux, demultiplexing

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