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  • Bowtie2 long index(.bt21) and tophat

    I am using tophat2 with long index with suffixes .bt21. But it is giving the following error

    HTML Code:
    Could not find Bowtie 2 index files (.*.bt2)

  • #2
    As of TopHat v.2.0.11 64-bit bowtie2 indexes were not supported. A new maintenance release is out (v. 2.0.12) but it is likely that long indexes are still not supported.

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    • #3
      Yes, I am using tophat/2.0.12 but still getting that error. Anyway, thanks for your reply.

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      • #4
        try to change "bt2" into "bt2l" in the tophat source file.

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        • #5
          Originally posted by pengchy View Post
          try to change "bt2" into "bt2l" in the tophat source file.
          @pengchy: Will this work by changing bt2 to bt2l in source?

          I am using tophat 2.1.0, still have problem of using bt2l. Any solutions so far? I am working on a very genome, so have to use bt2l. Can I align each chromosome separately, and then merge the bam files?

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          • #6
            Originally posted by yifeng View Post
            @pengchy: Will this work by changing bt2 to bt2l in source?

            I am using tophat 2.1.0, still have problem of using bt2l. Any solutions so far? I am working on a very genome, so have to use bt2l. Can I align each chromosome separately, and then merge the bam files?
            Yes, I have tested this on tophat-2.0.13.Linux_x86_64/tophat successfully.

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