Last updated: 2017-11-08

Code version: 9a86ba3

In this analysis I will explore the UMI usage in the Net-Seq1 library. Due to low read counts in the total sample, I will exclude this sample from the anaysis.

This code is used to create a text file that I can explore in R. It has a list of all of the UMIs used for the sample sorted by usage with the number of times each is used. This is run before the duduplication step.

samtools view {file} | tr "_" "\t" | cut -f 2 | sort | uniq -c > ../../output/UMI_{file}_stat.txt

All files have been create. Will import to R when I can mount midway on my computer.

sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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     

loaded via a namespace (and not attached):
 [1] compiler_3.4.2  backports_1.1.1 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.2     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.13   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      git2r_0.19.0   
[13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1

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