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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Utilizing --user_bowtie #42

Closed nsmt89 closed 4 years ago

nsmt89 commented 4 years ago

Hi, I want to use --user_bowtie function but I can't seem to successfully put it in command line. Do I need to specify the path? If I do, how to put it in the command line?

Thank you

mrmckain commented 4 years ago

For that option, you need to create the bowtie indices yourself and then give the option the path to the base name you used. For example, if you use a file call mysequence.fasta to make the bowtie indices and the file is in a place called /usr/mybin, then you would need to give the option the entry /usr/mybin/mysequence.fasta . This assumes that your bowtie indices are in the same directory as your sequences and that you didn't use a different base name. If you did, change accordingly.