Goals
The goal of this tutorial is to demonstrate how to use Synapse Synapse can manage files and track processing steps in an RNA-Seq workflow to manage files and track processing steps.
Getting Raw Data
The first step is to download the data onto the computer where you will be processing it.
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# 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 then use the alignment tool of your choice to map these reads. We will use STAR to map the reads.
Setting Up the Local Environment
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mkdir demo-rnaseq-workflow #dir to store the STAR genome index for the reference genome mkdir ref-genome |
Creating a Genome Index
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# 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
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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 |
Let’s store Store the results and provenance in Synapse.
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