Last updated: 2021-04-30

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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”

https://r4ds.had.co.nz

ggplot2 Quickref

http://r-statistics.co/ggplot2-cheatsheet.html

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