Bioinformatics Online Courses
Ashish kumar Choudhary (Scientist, strandls, IITB)
Activity: Complete Bioinformatics Course
Instructions
Join our course for a seamless learning experience! No more juggling disconnected tutorials or
deciphering confusing instructions. Our meticulously structured program offers concise,
comprehensive lectures, seamlessly blending theory with practical application.
(https://www.youtube.com/@bioinfobyte)
Week Domain name Module Topics/Concepts Learning Outcome(s)
1 Linux commands Module 1 Introduction to Unix • Intro to the command line
and shell scripting environment • Linux file system
• Viewing and editing files
• Learning basic commands:
basic commands: man, echo,
ls, pwd, mkdir, rmdir, mv, cp,
open, touch, cat, find, tail, wc,
clear, diff
1, 2 Module 2 Mastery of Linux • Use of vim, grep, less, cut, join,
command line sort, sed, awk command
tools • Use of samtools, bedtools
commands
• Using the above commands to
handle the biological data
2 Module 3 Shell scripting • Introduction to Bash Shell
Scripting
• Variables and read user inputs
• If statements and comparisons
• Positional parameters and for
loops
• Functions and arithmetics
• File conditions
• While loops
3 Practice • Practice Questions
Module
3 Git Tutorial for Module 1 Introduction to git • Basic terminology
Beginners • Clone repository.
• Git commands: git commit, git
push, git pull, git stash, undo
git commit, delete remote
branch
4 Database Module 1 Handling Biological • Accessing publicly available
handling database NGS experimental data from
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Bioinformatics Online Courses
Ashish kumar Choudhary (Scientist, strandls, IITB)
Gene Expression Omnibus
(GEO)
• Accessing publicly available
NGS experimental data from
the Sequence Read Archive
(SRA)
• Accessing genome reference
data (NCBI, Ensembl, and
UCSC)
5,6,7 Coding language Module 1 Introduction to R / • R/python syntax
Introduction to • Data types and data structures
Python • Data inspection and wrangling
• Use package built-in functions
• Perform data manipulation and
visualization
8 Module 2 Coding Practice • Coding test series
Exercises
9,10 NGS Data Module 1 Introduction to NGS • Sequencing, basic terminology
analysis • sequencing depth, Types of
high throughput data
• Basic sequencing workflow
• Genomics file formats: fasta,
fastq, sam, bam, cram, bed,
vcf, gtf, gff3
• Difference between different
normalization methods
• RPKM/FPKM/TPM/log-
normalize/ ST normalization
11 Module 2 RNA seq analysis • End-to-end RNA seq analysis
with 1 data
12 Module 3 scRNA seq analysis • End-to-end scRNA seq analysis
with 1 data
13 Data • Basic ggplot2 syntax and
Visualizations creating a basic plot
• Visualize gene expression data
using ggplot
• Heatmaps
• Scatter plot
• Box plot
• Customizing plots using scales
and colors
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