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 22.214.171.124 (ERR): "Bowtie2Index/rRNA" does not exist or is not a Bowtie 2 index Exiting now ...
Does anyone have any ideas? Thanks!