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Gregg Randolph

Gregg Randolph

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Pooling for CU sequencing:

Code Block
library(tidyverse)
AmfReads <- read.csv("/Users/gregg/Downloads/AMF1_Test_filtermergestats.csv", header = FALSE)
Map <- read.csv("/Users/gregg/Downloads/Bo_Stevens_Sample_Positions.csv", header=TRUE)
Map <- Map[,c(1,2,4)]
Map$order <- c(1:96, 1:92)
AMFmeta <- data.frame(do.call('rbind', strsplit(as.character(AmfReads$V1),'.',fixed=TRUE)))
AmfReads <- cbind(AMFmeta$X2, AmfReads[,2:4])
names(AmfReads) <- c("Sample.ID", "Reads", "Reads2", "Reads3")
AmfReads <- inner_join(AmfReads, Map, by = "Sample.ID")
LowAmf <- AmfReads[ which(AmfReads$Reads < 500),]
write.csv(LowAmf, "/Users/gregg/Downloads/LowAmf.csv", quote = FALSE, row.names = FALSE)

AMF1_Test_filtermergestats.csv Bo_Stevens_Sample_Positions.csv

Sample.ID

Reads

Reads2

Reads3

Plate.Position

Plate

order

A26

35

26

18

A9

2

65

A27

42

20

15

B9

2

66

A29

16

7

4

C9

2

68

A30

36

24

11

D9

2

69

A31

40

20

15

E9

2

70

A32

28

18

11

F9

2

71

A34

36

12

8

G9

2

73

A35

34

18

10

H9

2

74

B3

392

248

149

G11

2

91

L108

77

47

32

F4

1

30

L54

70

33

19

F7

1

54

L88

416

236

143

A4

1

25

LB1

104

51

34

A2

1

9

LB2

164

107

45

F3

1

22

LB3

70

35

20

C5

1

35

LB4

308

194

159

H6

1

48

LB5

310

169

129

E8

1

61

LB6

118

68

50

B10

1

74

LB7

374

219

161

G11

1

87

Since the test sequencing included all samples, we are adjusting pooling for samples that both replicates returned less than 500 reads each. These samples will be pooled at a volume of 20 ul while all others will be pooled at 2 ul. 2 ul from all was combined into one column of strip tubes. 18 ul was added by well pattern above. Tubes were vortexed and centrifuged. 100 ul was added from each strip tube to a 1.5 ml tube which was vortexed and centrifuged before 40 ul was transferred to a tube for shipping.