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Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
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gravatar for Sean Davis
2.1 years ago by
Sean Davis20k
United States
Sean Davis20k wrote:

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
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Sean Davis20k

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.

ADD REPLYlink written 2.1 years ago by Diego Diez700
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