| layout | title | subtitle |
|---|---|---|
page |
RNA-seq Tutorial Outline |
Temporary Overview |
SRA Toolkit Fastqc multiqc trimmomatic Kallisto R o Tximport o DESeq2
o Examining data on SRA Database o https://datacarpentry.org/organization-genomics/03-ncbi-sra/index.html o Download from SRA using fastq-dump o Examining Read quality
- FASTQC for quality control metrics
- summarise FASTQC with multiqc o https://datacarpentry.org/wrangling-genomics/02-quality-control/index.html o Trimming and Filtering
- Trim reads using trimmomatic o https://datacarpentry.org/wrangling-genomics/03-trimming/index.html o Pseudalignment using kallisto o Pseudoalignment vs alignment o <<kallisto.pdf>> o <>
o Import DESeq2 into RNA-seq o https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-gene-expression/dge-analysis-with-salmon-input o https://lashlock.github.io/compbio/R_presentation.html
o Introduction to shell o https://datacarpentry.org/shell-genomics/ o https://linuxjourney.com/lesson/the-shell o Introduction to R o https://datacarpentry.org/genomics-r-intro/