Data set selection
We will try and analysis this data.
GEO dataset GSE128010 studies the effect of the knock-out of gene SPP381 in Saccharomyces cerevisiae.
The data is paired-end! You need to adapt the pipeline!
- Create a new folder in ~/rnaseq_course
- Download raw data from SRA Run Selector with fastq-dump
- Back up: you can alternatively download the data with wget from: https://public-docs.crg.es/biocore/projects/training/PHINDaccess2020/miniproject
- Quality control of the data with FastQC.
- Decide if you need to trim the data! If so, use skewer.
- Retrieve genome reference genome and annotation files from ENSEMBL: ENSEMBL also provides fasta files for transcripts in the cdna folder of the FTP.
- Prepare SALMON index.
- Map data with SALMON
- Proceed with the differential expression analysis with DESeq2: import data, fit model, extract diffferential expression of WT vs KO, build dendrogram and run PCA. Filter genes.
- If any time is left, explore what kind of functional analysis you can run on this data set.