Description Usage Arguments Details
View source: R/RNASeqPipelineR.R
Builds a reference genome at 'path/Reference_Genome/'
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path |
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gtf_file |
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fasta_file |
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isoformsFile |
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name |
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doSTAR |
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starPath |
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threads |
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You must specify the Utils path if it is not already defined, and have your genome in a folder titled 'Reference_Genome'. This function will construct the reference genome using RSEM tools. The command line is the default shown in the documentation. 'rsem-prepare-reference –gtf gtf_file –transcript-to-gene-map knownIsoforms.txt –bowtie2 fasta_file name' or if doSTAR=TRUE 'rsem-prepare-reference –gtf gtf_file –transcript-to-gene-map knownIsoforms.txt –star –star-path starPath fasta_file name' If the gtf_file is not give, then the transcript-to-gene-map option is not used either. A fasta_file and a name must be provided.
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