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  • Bowtie vs BWA

    Hi All,
    I have illumina genomic sequencing data of a bacteria. When I aligned with bowtie only 1% aligned but using BWA (gap aligned) 76% aligned. The alignment showing lots of 1 nucleotide gaps on almost every 100 bp distance. Any suggestion what actually happening and how I handle this. Thank in advance

  • #2
    What's your estimated fold coverage?

    Comment


    • #3
      @GW_OK
      Could you kindly tell me how I calculate estimated fold coverage?

      Comment


      • #4
        Bowtie may still not support indels when doing alignment. I'm not sure, this may have been fixed (they "interoperate with indel callers", however).

        Search the world's information, including webpages, images, videos and more. Google has many special features to help you find exactly what you're looking for.

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        • #5
          What is the genome size ? How much coverage were you expecting ? As Richard says I would aim for an indel capable aligner.

          For bacteria I've had best results with Stampy or Novoalign to date.

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          • #6
            Originally posted by sarbashis View Post
            @GW_OK
            Could you kindly tell me how I calculate estimated fold coverage?
            How many bases sequenced divided by estimated (or known) genome size equals fold coverage.

            If you have something ridiculously high I can see where you might run into problems.

            But the fact that bowtie doesn't do indels is also a very, very good point.

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            • #7
              @GW_OK,
              Thanks for you help. The genome size is approx 5MB and my fold coverage is 262.4. Using BWA, my average read depth (sum(depth in all position)/ Genome size ) is 161.8.

              @colindaven,
              Novoalign is not open source. I have tried stampy-1.0.13 but it showing error Could not import the maptools module. I am not able to find out which module I have to install.

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              • #8
                That's a pretty high depth of coverage. You might try subsampling your data and see how that works.

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                • #9
                  @GW_OK, Thank you for your response. I will do a sampling of the data. I will take sample size of 60x coverage. Could you tell me why high depth coverage is not good.

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                  • #10
                    I can't believe anyone would use a gapless aligner, for anything.

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                    • #11
                      With high depth of coverage I think you can run into the error rate of the sequencer itself, leading to lots and lots of artifacts, like your every-other-nucleotide phenomenon.

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                      • #12
                        @GW_OK, I have done sampling on the basis of very high quality reads and got good alignment. earlier what I got are actually sequencing error. Thank a lot.

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                        • #13
                          Originally posted by Richard Finney View Post
                          Bowtie may still not support indels when doing alignment. I'm not sure, this may have been fixed (they "interoperate with indel callers", however).

                          http://www.google.com/search?hl=en&q...&aqi=&aql=&oq=
                          Hi Richard,

                          May we have a bit more information to do "gap alignment" with bowtie?
                          If it's possible, it will be a great reason to replace my aligner! (bwa to bowtie)

                          Thanks in advance,

                          Comment

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