Taj Azarian EpiDemos82

Assistant Professor, Genomics and Bioinformatics Cluster, Burnett School of Biomedical Sciences

EpiDemos82 / gist:80bf495bf1e339c542737a6f9ef565ed

Last active February 14, 2019 20:20

Lab naming scheme

	Good Practices
	1) It uniquely identifies the source of the sample (the location, the biological individual), or at least can be traced back to this information.
	2) It is clear and cannot be confused with any other sample in the same project, lab, department, university, universe.
	3) It is impossible to mis-write or mis-read.
	4) It is short.

	-Study (2-3 letter) or code as a study number
	CF
	CAR
	IH

EpiDemos82 / InterCladeGeneticDistance.R

Last active August 27, 2017 20:02

Mean SNP/genetic distance between groups/clades using R

	library(ape)
	library(vegan)
	library(adegenet) #Might as well load if you are doing phyo stuff

	setwd("/Users/../floder")

	Alignment <- read.dna("mfa.fasta",format = "fasta") #Importing alignment in fasta format
	fasta.seq.labels <- as.data.frame(labels(Alignment)) #Obtaining ordered taxa
	colnames(fasta.seq.labels) <- "taxa"
	clades <- as.data.frame(read_delim("~/clade_assignments_for_tax.txt")) #importing clade assigns for each isolate (in the future this could be automated using PCA)

EpiDemos82 / Useful_BASH_commands.txt

Last active March 1, 2023 19:01

Useful BASH commands for working with NGS data

	##GENERAL TEXT OR FILE MANIPULATION

	#Find lines in a list (e.g. file names) that are not present in another list
	#This is good for checking whether downstream files are present (i.e. pipeline ran susscessfully)
	comm -23 <(sort All.txt) <(sort Finished.txt)

	#Looping over anything
	for f in $(cat names.txt); do whatever to ${f}; done

	#renaming file extensions using bash code