Combined Lane QC

Last updated: 2019-02-15

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Knit directory: threeprimeseq/analysis/

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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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 [5] magrittr_1.5     tidyselect_0.2.4 munsell_0.5.0    colorspace_1.3-2
 [9] R6_2.3.0         rlang_0.2.2      stringr_1.4.0    plyr_1.8.4      
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[17] git2r_0.24.0     htmltools_0.3.6  assertthat_0.2.0 lazyeval_0.2.1  
[21] yaml_2.2.0       rprojroot_1.3-2  digest_0.6.17    tibble_1.4.2    
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[33] stringi_1.2.4    compiler_3.5.1   pillar_1.3.0     scales_1.0.0    
[37] backports_1.1.2  pkgconfig_2.0.2

Combined Lane QC

Briana Mittleman

7/27/2018