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
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prasanthgopinathangs •
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.
Thank you satya. "Address of the genome "..i haven't still started the alignment .Yet thanks for providing the information.
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it is a separate executable called bowtie2-build which builds the index and not bowtie2 alone. The command should be bowtie2-build input.fa
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
You are missing a critical
-between the words bowtie2 and build. Your command should beThanks a lot for the help . i got the results. The explanation was very useful .