RNA-Seq - Githubissues

bhklab / handbook

Lab Handbook For BHKLab

https://bhklab.github.io/handbook/dev

1 stars 0 forks source link

RNA-Seq #67

Open jjjermiah opened 1 week ago

jjjermiah commented 1 week ago

Hackathon

[ ] #68
[ ] Data Types

Future work:

[ ] Get Familiar with Data Types and Outputs
- [ ] Identify common data outputs: FASTQ, BAM/SAM, and count matrices.
- [ ] Describe the purpose of normalized counts (e.g., TPM, FPKM, RPKM).

Resources To Be Described:

Software & Tool Documentation

[x] STAR - Spliced Transcripts Alignment to a Reference
A popular RNA-Seq aligner.
[ ] HISAT2 - Hierarchical Indexing for Spliced Alignment of Transcripts
Fast and memory-efficient tool for RNA alignment.
[ ] DESeq2 and EdgeR
Widely used R packages for differential expression analysis, available on Bioconductor.

Practical Datasets To Be Described:

[ ] The Cancer Genome Atlas (TCGA)
[ ] GEO (Gene Expression Omnibus)
[ ] EGA

some inspiration:

https://koesterlab.github.io/data-science-for-bioinfo/data_analyses/differential_expression.html