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  • Software packages capable of aligning roughly 9000 bp

    I am currently working
    Last edited by josecolquitt; 05-17-2010, 11:03 AM.

  • #2
    you'll probably need to give a few more details if you expect to get any help.. I this one 9000bp contig, 900 100bp Illumina reads, something else?

    To what genome are you trying to align these bases?

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    • #3
      bwasw. it works for 100bp-100kbp, against the human genome.

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      • #4
        Originally posted by josecolquitt View Post
        I am currently working

        While the topic is interesting - I think your forum etiquette is a bit... well let's just say it's unconventional. You'll have to be more specific than that if you want to engage with others and get feedback.

        On a side note - it is nice to see there are aligners that can handle longer reads, considering what the future brings!

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        • #5
          Problems with Mosaik package

          My apologies, I was attempting to delete the entire entry and revise. I am currently working with Simian Immunodeficiency Virus short reads obtained from 454. I am working at an internship trying to gain experience in the bioinformatics field. I am trying to use the Mosaik package in an attempt to sequence these short reads. However, I am having problems with the initialization of this package. Inside the read-me is a tutorial of sorts that guides the user through a demo of the command lists, and then gives a tutorial working with a sample set of C. elegans chromosome 2 reads.

          When I attempt to click on any of the programs within the bin directory, a pop up window will display for a fraction of a second and then disappear. I am quite sure that this is simply a result of my inexperience with these programs. Any help or guidance would be greatly appreciated.

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