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  • Blastn Results - analysis

    Hi Everyone,

    I have done some blasting on a draft genome that I assembled de novo(~300,000 contigs) and now I want to analyze the results. I used blastn, and I really want to see what was found in the blast results. Blast2GO doesn't help with this (I believe its because I didn't blastx or blastp)

    SO, my question is, can anyone give me an idea on what program I can use to manipulate/analyze the results so that I can look at the stats of the top hits, etc?
    My blastn results are in tabular format. Any ideas will be extremely helpful.

    Thank you!

  • #2
    Originally posted by NGS_New_User View Post
    I used blastn, ... Blast2GO doesn't help with this (I believe its because I didn't blastx or blastp)
    Correct, Blast2GO wants either BLASP or BLASTX against the NR protein database.

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    • #3
      Originally posted by NGS_New_User View Post
      SO, my question is, can anyone give me an idea on what program I can use to manipulate/analyze the results so that I can look at the stats of the top hits, etc?
      My blastn results are in tabular format. Any ideas will be extremely helpful.
      What kind of stats? If you just want the top hit, you can tell BLAST to only give you one hit per query.

      Comment


      • #4
        Originally posted by maubp View Post
        What kind of stats? If you just want the top hit, you can tell BLAST to only give you one hit per query.
        The kind of summary stats I am aiming for or rather looking to extract is kinda similar of what is outputted by blast2go, ie in terms of top hit species and species distribution.
        So, I was wondering if there is any other program out there that I can feed the BlastN results to get the stats. Or if anyone has a script to share that I can use to manipulate the data and extract such results.

        Comment


        • #5
          BLAST 2.2.28+ or later has the option of outputting the species name in the tabular output:
          This is an open letter to the NCBI BLAST+ team to request two simple enhancements which I think would be extremely useful - first and foremo...


          You might also be interested in "blobology" from the Blaxter lab:
          Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED) - blaxterlab/blobology

          Comment

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