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The goal of this tutorial is to demonstrate how Synapse can manage files and track processing steps in an RNA-Seq workflow.

Getting Raw Data

The first step is to download the data onto the computer where you will be processing it.

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Code Block
# Get brain fastq file
synapse get syn2468554

# Get adrenal fastq file
synapse get syn2468552

Map the Raw Reads

Now that we have the data, you can use the alignment tool of your choice to map these reads. We will use STAR to map the reads.

Setting Up the Local Environment

Code Block
mkdir demo-rnaseq-workflow

#dir to store the STAR genome index for the reference genome
mkdir ref-genome

Creating a Genome Index

Code Block
# the reference genome
# downloads as hg19_chr19_subregion.fasta
synapse get --downloadLocation ref-genome/ syn2468557

#create a STAR genome index
STAR --runMode genomeGenerate --genomeDir ref_genome --genomeFastaFiles ref-genome/hg19\_chr19\_subregion.fasta

Map Adrenal and Brain Tissue Reads

Code Block
star --runThreadN 1 --genomeDir ref-genome/ --outFileNamePrefix brain --outSAMunmapped Within --readFilesIn brain.fastq

star --runThreadN 1 --genomeDir ref-genome/ --outFileNamePrefix adrenal --outSAMunmapped Within --readFilesIn adrenal.fastq

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