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Old 12-29-2015, 06:48 PM   #1
antifolate
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Default 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.
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Old 12-30-2015, 12:46 PM   #2
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Hello everyone!

Please help.

Thanks!
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Old 12-30-2015, 02:20 PM   #3
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Comma/tab delimited formats are used for ease of programmatic parsing. What kind of visualization do you want to generate with those formats?
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Old 12-30-2015, 02:39 PM   #4
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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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Old 12-31-2015, 08:20 AM   #5
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It may be worth looking into converting the results into a bed file and then use that for visualization.
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Old 01-06-2016, 07:55 AM   #6
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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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Old 01-06-2016, 11:40 AM   #7
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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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