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