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  • Bowtie2 and fasta format input

    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!

  • #2
    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.

    Comment


    • #3
      Converting to .fa or .fsa or even .fasta doesn't work and gives me the same errors :\

      Comment


      • #4
        Not sure why you are using -U. How about:
        Code:
        $ bowtie2 -f ACGE01.1.fsa_nt -x agaA -S ACGE01.sam

        Comment


        • #5
          That doesn't work either :|

          Comment


          • #6
            It is working for me with v.2.2.3. What version of bowtie2 are you using?

            Comment


            • #7
              Are you sure it's in the working directory and had read permission set?

              Comment


              • #8
                Ah yes, my read permissions were wrong. Thank you for the help!

                Comment

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