Bowtie2 and fasta format input

[aakriti]

Hello all,

I am trying to make an alignment using Bowtie2 on the following contigs data: http://www.ncbi.nlm.nih.gov/Traces/w...ACGE01#contigs

I downloaded the file that is in the .fsa_nt format, since I thought I could use fasta formats as an input for Bowtie2 using the following command:

$ bowtie2 -f -x agaA -U ACGE01.1.fsa_nt -S ACGE01.sam


However, I keep getting the same error no matter what I do:

Warning: Could not open read file "/ACGE01.1.fsa" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1

Has anyone else run into a similar problem or have any advice on what I can do instead?

Any help will be very appreciated!

Thanks!

[Brian Bushnell]

I can't remember if Bowtie2 supports fasta read input, but if it does, the problem may be the filename. Looks like it is truncating "fsa_nt" to just "fsa". "fsa_nt" is a non-standard extension anyway; try renaming it to ".fa" instead.

[aakriti]

Converting to .fa or .fsa or even .fasta doesn't work and gives me the same errors :\

[GenoMax]

Not sure why you are using -U. How about:

$ bowtie2 -f ACGE01.1.fsa_nt -x agaA -S ACGE01.sam

[aakriti]

That doesn't work either :|

[GenoMax]

It is working for me with v.2.2.3. What version of bowtie2 are you using?

[Brian Bushnell]

Are you sure it's in the working directory and had read permission set?

[aakriti]

Ah yes, my read permissions were wrong. Thank you for the help!