Entering edit mode
http://rpubs.com/seandavi/KallistoFromR
In this little workflow, we will be using a relatively new technology, pseudoalignment and quantification to deal with RNA-seq data from eight samples. The technical steps are:
- Use the SRA SDK to download FASTQ files for each sample
- Build a transcriptome index for Kallisto
- Pseudoalignment and quantification with Kallisto
- Read Kallisto output into a
SummarizedExperimentobject
Technical skills being showcased include:
- Accessing data from SRA using R/SRA SDK
- Use of R
system()functionality to orchestrate workflows involving command-line programs - Parallel processing with BiocParallel
- RNA-seq processing with Kallisto
Great tutorial. I found that the "abundance.txt" file referred to before the call to runKalllisto() is actually called "abundance.tsv". After making that change everything runs smoothly.