i am new the area of bioinformatics . Right now working on the tuxedo protocol . Trying to analyze a data based on the e coli reference genome. 




this is my file  location   -  **/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index$ ls
reference_genome.fa**



 when i run the command   -----**bowtie2 build ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome.fa**



This is the error that comes up 


**Could not locate a Bowtie index corresponding to basename "build"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align --wrapper basic-0 build /home/ubuntu08/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome.fa 
bowtie2-align exited with value 1**





i understand the problem with the location of file. But i am not able to solve the issue even after maintaining the reference genome in the same folder ..


ps: i am a beginner to the area of bioinformatics
Microfuge is right. Your command should be

    bowtie2-build -f ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome.fa ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome

Then ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome is the address of your index. You can provide it at the time of alignment.