Introduction to RNAseq
1
Genomics
1.1
Sequence
1.2
Read sequence
1.3
Contig sequence
1.4
Summary
2
Bioinformatics file formats
2.1
Introduction
2.2
What is a file format?
2.3
Annotation files
2.4
Glossary
3
Reference sequence
3.1
FASTA
3.2
Exercise
3.3
Rule of thumb
4
Gene annotation
5
Raw data
5.1
Introduction
5.2
FASTQ
5.3
Unix tooling
6
RNAseq bioinformatics workflow
6.1
Adapter trimming
6.2
Alignment
6.3
Read counting
6.4
RNAseq checklist
6.5
Summary
7
QC
7.1
Number of mapped reads
7.2
STAR aligner
7.3
Number of assigned reads
7.4
FastQC
7.5
Intragenic vs Intergenic region
7.6
Reads mapping bias
7.7
Insert size distribution
7.8
Where to look for more help
8
All about RNAseq
8.1
General
8.2
Technology
8.3
Differential expression (DE)
9
Lesson plan
10
Meeting notes
Introduction to RNAseq
4
Gene annotation
As discussed in [reference genome] module. The reference genome is just a string of charaters.
