Fasil Kebede
Location Ethiopia
Activity
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Fasil Kebede made a comment
How can we get the certificate for this course? Is this course sponsored or we need to pay $49 to upgrade (if we qualify)? Please advise on next steps.
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Fasil Kebede made a comment
I have received instructions to earn my Certificate through my email. Thank you!
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Fasil Kebede made a comment
Thank you all educators and the sponsors of the course.
I have enjoyed the course and learnt a lot. -
Thank you for the valuable information. STHDA is superb!
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Fasil Kebede made a comment
Q1. All produce the same output
Q2. Option 3
Q3. facet_wrap(~Species, scale='free_y') +
labs(x = "Sepal Length", title = "Petal vs Sepal Length") -
Beautiful graphs for publication.
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data=iris (NOT data=Iris)
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Fasil Kebede made a comment
boxplot(iris)
boxplot(Petal.Width ~ Sepal.Width, data=iris)
boxplot(Petal.Width ~ Sepal.Width, iris, col="#add8e6", border="#2f4f4f", main="Boxplot Peal.Width
vs. Sepal.Width") -
check <- test.col == FALSE
nrow(check)check2 <- test.col$Test == FALSE
check2 -
Fasil Kebede made a comment
setosa1 ==setosa.sub1
str(setosa.sub2) -
x <- c(3,10,30)
m <- rep(x, times=2)
n <- c(x,0,x)
m==n
length(m)
length(n) -
Fasil Kebede made a comment
#Create dataframe
Fruits <- c("Apple","Banana", "Orange", "Mango")
Price <- c(4,3,2,8)
Nature <- c("Local", "Exotic", "Local", "Exotic")
dataframe <- data.frame(row.names = Fruits,Price,Nature)
str(dataframe)#Checking dataframe
dataframe (Ctrl+enter)
levels(dataframe$Nature)
nlevels(dataframe$Nature)#Data...
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Data visualization is a blend of science and art. It should be trustworthy, accessible and elegant. I like the philosophy and the three principles.
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Fasil Kebede made a comment
I found the bash scripting in week 2 very important. The contents are generally good enough for an introductory course.
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Fasil Kebede made a comment
Definitely I will use the concepts I learnt to carry out study. I am preparing myself to work on a remote server (HPC) and this course will no only allow me to prepare my own scripts, but also help read and understand those which have already been written by experienced bioinformaticians in a collaborative project.
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All principles listed are valuable. I wonder if it is possible to document somewhere type/version numbers of the most important software used in the analysis.
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#!/usr/bin/env bash
#wildcard for all.bam files
for file in *.bam
do
#produce error log such as if file is empty
set -eux
#use loop to count number of alignments in each .bam file
alignmentsthree=$(samtools view -c $file)
#return filename and number of records to user
echo "number of alignments in $file=$alignmentsthree"
done -
Fasil Kebede made a comment
Very useful.
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Fasil Kebede made a comment
The ShellCheck is cool.
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When we work on high performance computer clusters with big data, tracking our progress and identifying errors early may help reduce cost.
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Fasil Kebede made a comment
#!/usr/bin/env bash
#Define a function to declare availability of a file
function file_exists() {
if [[!-e$1]]; then
echo "file does not exist:$1"
fi
} -
Fasil Kebede made a comment
#!/bin/bash
for((i=1;i<=5;i++))
do
if [[ $i -eq 2 ]]; then
echo "fizz"
else
echo "buzz"
fi
done#To avoid syntax error near unexpected token 'then', there must be a space between if and [
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Fasil Kebede made a comment
#!/usr/bin/env bash
read -p "Please enter a diamond cutyou want:" quality
#If user enters Fair or Good, return Insufficient quality to proceed
if [[ ${quality}=="Fair" ]] || [[ ${quality}=="good" ]];then
echo "Insufficient quality to proceed"
elif [[ ${quality}!="Ideal" ]] && [[ ${quality}!="Very Good" ]] && [[{ $quality}!="Premium" ]];then
#If... -
Fasil Kebede made a comment
#!/usr/bin/env bash
animal="$1"
case $animal in
cow)
echo "Here, moo"
;;
sheep)
echo "There a baa"
;;
duck)
echo "Everywhere a quack"
;;
*)
echo "Old MacDonald had a farm"
;;
esac#in the terminal
chmod +x farm.sh
./farm.sh camel
#Output
“Old... -
Fasil Kebede made a comment
#!/usr/bin/env bash
#a variable called temperature
temperature=$1
# variables called minimum and maximum temperatures
mintemp=10
maxtemp=30
#returns too hot if temperature is greater than 30
if [[ ${temperature} -gt ${maxtemp} ]]; then
echo "Too hot!"
#returns too cold if temperature is less than 10
elif [[ ${temperature} -lt ${mintemp} ]];... -
Fasil Kebede made a comment
#!/usr/bin/env bash
#create a bash script with .sh file extension fruits.sh
#the list of fruits
fruits=("pineapple" "peach" "raspberry" "plum" "apple" "kiwi")
#number of fruits
echo "number of elements are ${#fruits[@]}"
#last element in the array fruit
echo "the last element is ${fruits[5]}"
#then to execute the bash script
bash fruits.sh -
Fasil Kebede made a comment
I liked the course contents for week1. Looking forward to learn new concepts and skills in week2. Thank you!
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Fasil Kebede made a comment
The lesson is very good. I had to watch a couple of YouTube videos to understand it better. I expect it will have many applications later on.
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Fasil Kebede made a comment
A very good tutorial on creating a soft link in one minute https://www.youtube.com/watch?v=_NXQF1IoViw
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Fasil Kebede replied to Cassidy Smith
If you are running ubuntu, you can download data by using Firefox web browser directly with this link ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/BfB_Linux_Bash_R/
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Fasil Kebede made a comment
Q1. Four file contain the word 'difference': ghandi.txt ghandi.txt.out ghandi_2.txt
grep -F difference ghandi.txt.out
Q2. The word “Premium” occurs 13791 times in the file diamonds_fix.txt
grep -o -i Premium Diamonds_fix.txt |wc -l
Q3. Out of a total of 53940 lines in the file diamonds_fix.txt, 41858 do not include the phrase “Very good”Total no. of...
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Fasil Kebede made a comment
sort fruit.txt | uniq -id >repeated_fruit.txt
Then to print what is inside this file:
cat repeated_fruit.txt
To open and see the new list in nano:
less repeated_fruit.txt -
Fasil Kebede made a comment
I checked: man sort
and found that we need two dashes before random:
sort -R fruit.txt - -random-source=/dev/random
Am I correct? -
Very valuable
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Fasil Kebede made a comment
I think the role of bioinformatics grows in the future even more when wet lab preparations of things like tissue samples get more and more automated. I'm also more interested in bioinformatics. I liked the analogy between bites per day and empty petri dishes/day in the above story. Nice transition.
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Fasil Kebede replied to Louise McN
I guess you need to first unzip your file with:
tar -zxvf All_data.tar.gzFor more, please read https://www.pendrivelinux.com/how-to-open-a-tar-file-in-unix-or-linux/
Alternatively, you may go directly to the unzipped file by: cd Week1_Data
Then type ls to see what is inside. -
What will happen when you lock your file in a windows environment? It cannot be opened and read by others. Similarly, when you work on a server, for example, you can only read/write/execute a linux machine when you receive those privileges by an admin. You can also protect your files in the same manner.
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Fasil Kebede made a comment
If you write the below, you can get the course data
wget -r -np ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/BfB_Linux_Bash_R/ -
It is good to introduce to fellow learners how they can install ubuntu virtually for example on their windows machine:
https://www.virtualbox.org/wiki/Download_Old_Builds_6_0
and add extension pack (additionally) if they wish to use flash drives on their virtual machine https://askubuntu.com/questions/661414/how-to-install-virtualbox-extension-packI...
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Fasil Kebede made a comment
I want to take the course to analyze biological/agricultural data as part of my graduate study requirement.