What is wrong with my bowtie2 index?
1
0
Entering edit mode
16 months ago
ksh4718 • 0

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!

bowtie2 rRNA • 588 views
ADD COMMENT
0
Entering edit mode
16 months ago
ATpoint 54k

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?

ADD COMMENT
0
Entering edit mode

Ah, that helped. Thanks!

ADD REPLY

Login before adding your answer.

Traffic: 1004 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6