What is wrong with my bowtie2 index?

Question

[ksh4718]

Hi all. I am trying to map mouse rRNA reads and so I made a bowtie2 index for the mus musculus rRNA genome. I downloaded all rRNA sequences from GenBank and made a FASTA file.

Here is my index code:

bowtie2-build -f RNA_musmusculus.fasta rRNA

The files for index were made (small index because it is just rRNAs):

  4.1M Jun 11 09:49 rRNA.1.bt2
 7.7K Jun 11 09:49 rRNA.2.bt2
  746 Jun 11 09:49 rRNA.3.bt2
 7.7K Jun 11 09:49 rRNA.4.bt2
 4.1M Jun 11 09:49 rRNA.rev.1.bt2
 7.7K Jun 11 09:49 rRNA.rev.2.bt2

And my mapping code is here:

index=Bowtie2Index/rRNA

bowtie2 -t -x $index --un 6234-S10_norRNA.fq.gz -1 $dir'6234-S10_paired_1.fq.gz' -2 $dir'6234-S10_paired_2.fq.gz' -S 6234-S10_mapped.sam

The directories are correct but I am getting this error message:

Bowtie2 2.3.5.1
(ERR): "Bowtie2Index/rRNA" does not exist or is not a Bowtie 2 index
Exiting now ...

Does anyone have any ideas? Thanks!

Answer 1

[ATpoint]

The path to it is most likely messed up. Is the script in a directory that contains a folder Bowtie2Index in which the index is located?

[ksh4718]

Ah, that helped. Thanks!