bowtie inspect error

Question

[Msadeghibiology91]

We inserted this command bowtie-inspect -s mm9 and got this error Could not locate a Bowtie index corresponding to basename "mm9" Command: bowtie-inspect --wrapper basic-0 -s mm9 what is it mean?

[Arup Ghosh]

Use the complete path to the index file with exact genome version suffix.

Answer 1

[Devon Ryan]

It means that mm9.1.bt2 and the other indexes for that genome aren't in your current directory. You probably want bowtie2-inspect /path/to/index/files/mm9.

Also, I assume you're actually using bowtie2, rather than bowtie (if not, stop doing that).

Answer 2

[Msadeghibiology91]

thank you dear Devon Ryan I get my answer