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  • Visualizing BLAST output

    What tools would you recommend to visualize blast tsv output? I found several ones but none of them work with tab (or comma) delimited formats.

  • #2
    Hello everyone!

    Please help.

    Thanks!

    Comment


    • #3
      Comma/tab delimited formats are used for ease of programmatic parsing. What kind of visualization do you want to generate with those formats?

      Comment


      • #4
        Something as simple as a line connecting matches would be enough. Or maybe coloring matches with the same color. Kablammo is an example, but it doesn't take tsv formats as input (http://kablammo.wasmuthlab.org/).

        As you said, tsv/csv formats are easier for parsing and manipulating. I've filtered the hits in the tsv output accoding to many criteria and would like to visualize those remaining hits.

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        • #5
          It may be worth looking into converting the results into a bed file and then use that for visualization.

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          • #6
            x=genetic distance from my genome , interval, maybe logarithmic
            y(x)=number of organisms in the database with that distance

            where to find that, how is it called ?

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            • #7
              For the record, I wrote Perl scripts to convert the filtered TSV output into pairwise format, using the original pairwise hits. I then used the pairwise output for visualization.

              Since I'm more interested in structural variations, a BED format wouldn't be really helpful.

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