rmindex (R Meyer index) is an R package that assesses and selects multiplex indexes from the Meyer and Kircher (2010) library protocol for use with illumina sequencing.
- install rmindex
install.packages("devtools")
install.packages("tidyr")
devtools::install_github("teasdalm/rmindex")
library(rmindex)
- Read barcodes and plot
# Read barcodes
# Example file in /data
barcode_df <- read_index("barcodes.csv")
# Plot barcodes
plot_barcodes(barcode_df)
# All in one
plot_barcodes(read_index("barcodes.csv"))
- Select random none overlaping indexes
# Select random barcodes defaults are shown
barcode_select(number_to_select = 6)
# example output
# Selected indexes B023 B029 B033 B039 B040 B046
# TCD_name Seq base1 base2 base3 base4 base5 base6 base7
#23 B023 GATCTCG G A T C T C G
#29 B029 CCGATTG C C G A T T G
#33 B033 CATCCGG C A T C C G G
#39 B039 CGAATGC C G A A T G C
#40 B040 TTCGCAA T T C G C A A
#46 B046 GTACCGG G T A C C G G
# Select and plot
plot_barcodes(barcode_select(number_to_select = 6))
- with more complex indexes
# Select random barcodes
barcode_select(indexes = c(1,4,63:100), number_to_select = 6)
# example output
#selected indexes B072 B085 B086 B087 B088 B093
# TCD_name Seq base1 base2 base3 base4 base5 base6 base7
#72 B072 GGCATAG G G C A T A G
#85 B085 CCGGATA C C G G A T A
#86 B086 GCCGCCT G C C G C C T
#87 B087 AACGACC A A C G A C C
#88 B088 CCAGCGG C C A G C G G
#93 B093 GACTTCT G A C T T C T
- MiSeq sample sheet test
sample_sheet_test("sample_sheet.csv")
-
Data folder includes...
- index.rda - 200 plus Meyer and Kircher (2010) indexes
- example_barcodes.csv - example index csv file
-
To load meyer index dataset
library(rmindex)
head(meyer_index)