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Old 07-28-2013, 03:52 PM   #1
angerusso
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Location: US

Join Date: Oct 2011
Posts: 47
Default Question: prioritizing fusion based on tophat result

How to prioritize fusions based on these columns?

Potential_fusions written by tophat-fusion-post writes these 5 columns but I don't what these columns really mean. Can anyone explain? E.g. I don't understand how can "reads" be less than "pe_reads". What is the difference between "pe_reads" and "pe_reads_span". What is reads_ctrd?

What is the priority order of these columns in order for me to identify which fusion to prioritize to be biologically meaningful? ANy help will be greatly appreciated!

reads pe_reads pe_reads_span reads_ctrd reads_left reads_right

5201 4465 588 9 85309 85184

4640 488 3279 5 289783 45

3394 13258 1764 1 36 62

Thanks.
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Old 08-08-2013, 02:39 AM   #2
kokonech
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Default

Hi,

I suppose potential_fusion.txt is an intermideate file. According to tophat-fusion documenation you should look on files result.txt or result.html, which contains the results. More details are here:
http://tophat.cbcb.umd.edu/fusion_manual.html#output

The columns are explained here:
http://tophat.cbcb.umd.edu/data/result.html#detail
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