Useful links for unix

• screen: stopped jobs / resume / kill. unix.stackexchange
• shell script - replace a character in a string: stackoverflow

Useful links for plots

R:

• ggplot2 tutorials: Edwin Chen's blog  CEB institute  Quick-R 
• Box plot: ggplot2
• Violin plot: ggplot2
• Multiple subplots:  sthda.com

Python:

• Plots: matplotlib
• Error in plot when DISPLAY is undefined: stack overflow.
• Drawing distribution line using histogram. stack overflow.

Tag SNP and Singleton SNP

Tag SNP:

A group of SNPs in a region of a genome may be in high linkage disequilibrium (LD). In such case, one SNP, called a tag SNP, represents the whole group. As sequencing SNPs is costly, often only the tag SNP, instead of the all the SNPs in the group, is sequenced to find genetic variation that may be associated with a phenotype.

Singleton SNP:

Sometimes one tag SNP represents only itself i.e., it is not in high LD with any other SNPs in that region. Such tag SNP is called a singleton SNP.

References:

1) Wikipedia, Tag SNP, accessed on 29 March 2015.

2) Xiayi Ke et al. (2008), Singleton SNPs in the human genome and implications for genome-wide association studies, European Journal of Human Genetics, 16, 506–515.

Scale parameter in probability distributions

A parameter s is called a scale parameter of a probability distribution when it follows the following property:

F(x|s,θ) = F(x/s | 1,θ)

Here, F is the cumulative distribution function (cdf) and θ represents other parameters in the distribution.

When the probability distribution function (pdf) is defined for all values, then s must follow the following property:

f_s(x) = f(x/s)/s

Here, f is pdf of the standard distribution, and  f_s is pdf of the scaled distributions.

Intuitively,  higher scale parameter means higher spread of the distribution. Standard normal distribution with different scales are shown in the following plot.

And, here is matlab code to generate the above plot.

scales = [5,2,1,0.5,0.3];
x = -10:.001:10;
for s = scales
    y = normpdf(x./s) ./ s ;
    plot(x,y);
    hold on
end
legend('scale=5', 'scale=2', 'scale=1', 'scale=0.5', 'scale=0.3')
title('Standard normal distribution with different scale parameters')

Useful Bioinformatics Links

• Samtools: 
• Install: sudo apt-get install samtools
• References
• Convert BAM file to Fastq: 
• Install picard: sudo apt-get install picard-tools
• Use SamToFastq command.
• Picard project page