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I am trying to build an index on kallisto on mac using R studio and have saved my FASTA file to my desktop, however, when I run kallisto index -i DI_mRNA.index DI_mRNA.fa.gz, there is an error saying Error: FASTA file not found DI_mRNA.fa.gz

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    $\begingroup$ In what way are you running Kallisto on R? My guess would be you are not in the same directory as the fastq file. You can find out the current working directory with getwd() and set it with setwd(). $\endgroup$
    – TW93
    Jun 9 '20 at 18:53
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As mentioned in a comment, your working directory lacks the fasta file.

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