Error while building index for ecoli referenc genome

Question

[prasanthgopinathangs]

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]

it is a separate executable called bowtie2-build which builds the index and not bowtie2 alone. The command should be bowtie2-build input.fa

[prasanthgopinathangs]

Thank you for the reply. But i think in the command given above i have entered it as " bowtie 2 build " on itself. And dont i need to include the file location ? if yes is it only the location within the directory or the whole system path ? Sorry again for the doubt. I know that these are the very basic error . But i want to solve the errors that arise. Thank you

[GenoMax]

You are missing a critical - between the words bowtie2 and build. Your command should be

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

[prasanthgopinathangs]

Thanks a lot for the help . i got the results. The explanation was very useful .

Answer 1

[Satyajeet Khare]

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.

[prasanthgopinathangs]

Thank you satya. "Address of the genome "..i haven't still started the alignment .Yet thanks for providing the information.