Description Usage Arguments Details
Builds a reference genome at 'Utils/Reference_Genome'
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path |
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gtf_file |
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fasta_file |
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star_threads |
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name |
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gff3 |
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additional_param |
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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' 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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