Tutorial:Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
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@sean-davis-490
Last seen 15 days ago
United States

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:

  1. Use the SRA SDK to download FASTQ files for each sample
  2. Build a transcriptome index for Kallisto
  3. Pseudoalignment and quantification with Kallisto
  4. Read Kallisto output into a SummarizedExperiment object

Technical skills being showcased include:

  1. Accessing data from SRA using R/SRA SDK
  2. Use of R system() functionality to orchestrate workflows involving command-line programs
  3. Parallel processing with BiocParallel
  4. RNA-seq processing with Kallisto
rnaseq biocparallel workflows sra Tutorial • 2.7k views
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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.

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