Herper

 

These exercises follow the material in the GitHub section of Reproducible R.

1. Lets setup an environment to do some basic counting for RNAseq. We will follow the example in the salmon guide, but we will modify it for S. cerevisiae to make it quicker as the genomes smaller.

• Install Salmon with Herper
• Download reference data from Ensembl (“http://ftp.ensemblgenomes.org/pub/fungi/release-56/fasta/saccharomyces_cerevisiae/cdna/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz”)
• Use with_CondaEnv() to build the salmon index
• Next lets download a yeast dataset. Here’s a link to a meiotic yeast RNAseq fastq file: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR180/065/SRR18072865/SRR18072865_1.fastq.gz
• Use with_CondaEnv() to quantify the yeast counts
• Save your conda environment with

library(Herper)
install_CondaTools(tools = "salmon", env = "rnaseq")

download.file("http://ftp.ensemblgenomes.org/pub/fungi/release-56/fasta/saccharomyces_cerevisiae/cdna/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz", "~/Desktop/Saccharomyces_cerevisiae.R64.fa.gz")

with_CondaEnv(new = "rnaseq", code = system2("salmon", c("index", 
                                                         "-t", "~/Desktop/Saccharomyces_cerevisiae.R64.fa.gz",
                                                         "-i", "~/Desktop/Saccharomyces_cerevisiae.R64_index")))

download.file("ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR180/065/SRR18072865/SRR18072865_1.fastq.gz", "~/Desktop/yeast_fastq.fastq.qz")

with_CondaEnv(new = "rnaseq", code = system2("salmon", c("quant",
                                                         "-i", "~/Desktop/Saccharomyces_cerevisiae.R64_index",
                                                         "-l", "A",
                                                         "-r", "~/Desktop/yeast_fastq.fastq.qz",
                                                         "-p", "8",
                                                         "--validateMappings",
                                                         "-o", "~/Desktop/yeast_quant")))

export_CondaEnv("rnaseq", "~/Desktop/my_yeast_salmon_conda_envrionment.yml")