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  • tophat2

    I am new to tophat2 and when I ran the tophat2 command:
    "tophat2 --b2-very-fast -p 8 /home/mbashyam/indexes/hg19index /home/mbashyam/reads/SRR222177.fastq"
    it gave an error initially:
    "Warning: Could not find FASTA file /home/mbashyam/indexes/hg19index.fa
    [2013-01-30 18:32:46] Reconstituting reference FASTA file from Bowtie index"

    But the program moved on with the alignment (and is still running).

    I have used the same index files for bowtie2 earlier so I know they are ok. I would be grateful if someone could explain this error; or maybe it is to be ignored?

  • #2
    You don't have a fasta file with the same name as the bowtie index.
    Tophat is only a little bit slower, because it makes an extra step by creating this reference fasta file. Nothing to worry about

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    • #3
      Originally posted by Jetse View Post
      You don't have a fasta file with the same name as the bowtie index.
      Tophat is only a little bit slower, because it makes an extra step by creating this reference fasta file. Nothing to worry about
      Thanks. My index file which I made for bowtie2 was called hg19.fa; my colleague renamed it to hg19index.fa and then the error disappeared.

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      • #4
        This warning disappears when the name of the fasta file is the same as the name of the index (both without the suffixes.

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        • #5
          Thanks. I am sorry I did not follow your comment. Which fasta file?

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          • #6
            The fasta file from which the bowtie index is made. When you have downloaded the bowtie index, and not created the bowtie index from a fasta file, you always get this warning.

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            • #7
              Thanks, I got it now

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