Bio326.misc
Marie Saitou
4/29/2021
Last updated: 2021-04-30
Checks: 7 0
Knit directory: Bio326/
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This workflow is based on Galaxy Training materials aimed for the two-hour courses in Bio326, NMBU 2021.
0. Goal of this workflow
Explore useful tips for genome analysis
We will learn: How to find relevant data sets from the public repository How to obtain gene function/evolution data (mostly for vertebrates) The overview of population genetics concept with R
1. Ensembl
1.1 Variant analysis within species with our data
Ensembl Variant Effect Predictor (VEP)
VEP determines the effect variants on genes, transcripts, and protein sequence, as well as regulatory regions. We will use sample B variant file to see where we observed variants in the functional genomics context.
VEP(Ensembl): https://www.ensembl.org/info/docs/tools/vep/index.html
Reference tutorial: https://www.youtube.com/watch?v=rSIG_OVzyLU&t=157s
Launch VEP web interface 
Specify reference 
Specify input data 
The input data is available at:
https://github.com/mariesaitou/Bio326/blob/master/docs/assets/BIO326-misc/sampleB.chr18.QUAL800.vcf
Explore results 
1.2 Evolutionary analysis of tumore-suppressor genes between species
Go to https://www.ensembl.org/index.html
Reference tutorial: https://www.youtube.com/watch?v=bTBLg0bIi98&t=250s
2. Raw sequence data repositories
Find data sets from a paper 
Firt, go to https://www.ncbi.nlm.nih.gov/ 
The same data is also available at ENA.
https://www.ebi.ac.uk/ena/browser/home
We can search data in ENA as well 
Study accession number and raw data. 
We can search for the original paper with the accession number to read the study detail. 
3. GTEx portal - Human Gene expression/splicing/eQTL database
Review of transcriptome analysis Reference video (StatQuest): https://www.youtube.com/watch?v=TTUrtCY2k-w&t=7s
GTEx Portal https://www.gtexportal.org/home/
Example: highly expressed genes in muscle 
Example: expression of CKM gene in various tissues 
eQTL data sets: What is eQTL?
Example: CKMT1A gene expression and a variant at chr5:43504700 
Splicing data sets 
Example: CKMT1A splicing variants and their expression in various tissues 
4. Rstudio (on Orion)
4.0 Accessible color design
Color-blind barrier-free color pallet - Color Universal Design Organization (CUDO), Kei Ito (University of Tokyo)
Use in R: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/
Simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/
4.1 Simulating of evolution/Visualization with ggplot2
https://cooplab.github.io/popgen-notes/#allele-frequencies
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/wright-fisher-model
The file is also available: as Rmarkdown and as html
Case studies:
The balance between selection and random drift
sBB<-0.02
Balancing selection (clasic case - sickle cell anemia against malaria parasites)
sAB<-0.02, sAA<-0.01
Admixture
n_AA <-50, n_AB<-0, n_BB<-50, sAA, sAB, sBB <-0
How about in larger populations?
(edit n_gen and n_AA, n_AB, n_BB. n_gen = sum of (n_AA, n_AB, n_BB))R + ggplot info: https://www.nmbu.no/course/STIN300
“Hands-on programming with R”
https://rstudio-education.github.io/hopr/
“R for data science”
ggplot2 Quickref
4.2 Make a shareble script
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 whisker_0.4 knitr_1.31 magrittr_2.0.1
[5] R6_2.5.0 rlang_0.4.10 fansi_0.4.2 stringr_1.4.0
[9] tools_4.0.2 xfun_0.21 utf8_1.2.1 git2r_0.28.0
[13] htmltools_0.5.1.1 ellipsis_0.3.1 rprojroot_2.0.2 yaml_2.2.1
[17] digest_0.6.27 tibble_3.1.1 lifecycle_1.0.0 crayon_1.4.1
[21] later_1.2.0 vctrs_0.3.7 promises_1.2.0.1 fs_1.5.0
[25] glue_1.4.2 evaluate_0.14 rmarkdown_2.6 stringi_1.5.3
[29] compiler_4.0.2 pillar_1.6.0 httpuv_1.6.0 pkgconfig_2.0.3