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File Version Author Date Message
html e5a8da6 Briana Mittleman 2018-07-30 Build site.
Rmd 422a428 Briana Mittleman 2018-07-30 add peak cove pipeline and combined lane qc

I want to use this analysis to run simple QC on the first 32 libraries now that we have 2 lanes per library.

First, I will look at the new map stats to see how many more reads/mapped reads the socond lane provided.

library(tidyr)
library(reshape2)

Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':

    smiths
library(ggplot2)
library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
library(workflowr)
This is workflowr version 1.2.0
Run ?workflowr for help getting started
comb_map=read.csv("../data/combined_reads_mapped_three_prime_seq.csv", header = T, stringsAsFactors = T)
comb_map$line=as.factor(comb_map$line)
mapped_melt=melt(comb_map, id.vars=c("line", "fraction"), measure.vars = c( "lane1_mapped", "comb_mapped"))
mapped_melt$line=as.factor(mapped_melt$line)

ggplot(mapped_melt, aes(y=value, x=line, by=fraction,fill=fraction)) + geom_bar(stat="identity", position = "dodge") + facet_grid(.~ variable)+ labs(y="Reads Mapped")

Version Author Date
e5a8da6 Briana Mittleman 2018-07-30

Next I want to look at the x more mapped reads we got by line and fraction

ggplot(comb_map, aes(x=line,y=combed_xrmappedmore, fill=fraction)) + geom_bar(stat="identity", position = "dodge") + labs(title="X more mapped reads in adding second lane", y="X more mapped reads")

Version Author Date
e5a8da6 Briana Mittleman 2018-07-30 


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.2.0 dplyr_0.7.6     ggplot2_3.0.0   reshape2_1.4.3 
[5] tidyr_0.8.1    

loaded via a namespace (and not attached):
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