Question: Error while building index for ecoli referenc genome
1
gravatar for prasanthgopinathangs
2.7 years ago by
prasanthgopinathangs50 wrote:

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

rna-seq alignment • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Satyajeet Khare1.3k • written 2.7 years ago by prasanthgopinathangs50
1

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

ADD REPLYlink written 2.7 years ago by microfuge1.1k

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

ADD REPLYlink written 2.7 years ago by prasanthgopinathangs50
1

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
ADD REPLYlink written 2.7 years ago by genomax67k

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

ADD REPLYlink written 2.7 years ago by prasanthgopinathangs50
3
gravatar for Satyajeet Khare
2.7 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Satyajeet Khare1.3k

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

ADD REPLYlink written 2.7 years ago by prasanthgopinathangs50
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