bowtie2 can't find index

Question

[Ric]

I got (ERR): "tdna" does not exist or is not a Bowtie 2 index despite the index has been created.

> bowtie-build -f T-DNA.fasta tdna
> ls -hla tdna.*
-rw-rw---- 1 x default 4.1M Nov 23 11:44 tdna.1.ebwt
-rw-rw---- 1 x default  636 Nov 23 11:44 tdna.2.ebwt
-rw-rw---- 1 x default   17 Nov 23 11:44 tdna.3.ebwt
-rw-rw---- 1 x default 1.3K Nov 23 11:44 tdna.4.ebwt
-rw-rw---- 1 x default 4.1M Nov 23 11:44 tdna.rev.1.ebwt
-rw-rw---- 1 x default  636 Nov 23 11:44 tdna.rev.2.ebwt
> bowtie2 -x tdna -U read.fq -S read.sam
(ERR): "tdna" does not exist or is not a Bowtie 2 index
Exiting now ...

What did I miss?

Thank you in advance,

[GenoMax]

If this data requires un-gapped alignments then you should use bowtie v.1 for both index creation and alignments.

Answer 1

[Jeffin Rockey]

Here index creation is with bowtie1 bulid whereas the alignment is attempted with bowtie 2.

Create index using bowtie2-build. That will solve it

[Ric]

Thank you it works now.