Last updated: 2017-11-06

Code version: 7eeb4e1

I will use this analysis to look at inital data QC and points of interests.

First I looked at the number of reads that mapp to the genome before and after deduplication UMI steps.

Sorted Bam files:
388305 Undetermined_S0_R1_001-sort.bam
5111260 YG-SP-NET1-18486-dep-2017-10-13_S4_R1_001-sort.bam
688 YG-SP-NET1-18486-total-2017-10-13_S5_R1_001-sort.bam
7775502 YG-SP-NET1-18508-dep-2017-10-13_S2_R1_001-sort.bam
8408777 YG-SP-NET1-18508-nondep-2017-10-13_S3_R1_001-sort.bam
12164551 YG-SP-NET1-Unk1_S6_R1_001-sort.bam

Deduplicated Bam files: 51460 Undetermined_S0_R1_001-sort.dedup.bam
211005 YG-SP-NET1-18486-dep-2017-10-13_S4_R1_001-sort.dedup.bam
205 YG-SP-NET1-18486-total-2017-10-13_S5_R1_001-sort.dedup.bam
252074 YG-SP-NET1-18508-dep-2017-10-13_S2_R1_001-sort.dedup.bam
275790 YG-SP-NET1-18508-nondep-2017-10-13_S3_R1_001-sort.dedup.bam
252305 YG-SP-NET1-Unk1_S6_R1_001-sort.dedup.bam

Session information

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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