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 09-18-2011, 09:24 PM #1 jaycekoh Junior Member   Location: sg Join Date: Sep 2011 Posts: 2 queries about tophat fusion output I have some queries about result.html, http://tophat-fusion.sourceforge.net/data/result.html, explanations of which I do not understand 9. Number of spanning mate pairs 10. Number of spanning mate pairs where one end spans a fusion 11. If you follow the the 9th column, it shows coordinates "number1:number2" where one end is located at a distance of "number1" bases from the left genomic coordinate of a fusion and "number2" is similarly defined Am I right to say that 9. represents the number of paired ends, with one end totally on one chromosome of a fusion, and the other totally on the other chromosome of a fusion? Would I also be right to say that 10. is the same as 9., except that 9. has no end spanning a fusion, and 10. has one end spanning. Which is to say that 9. and 10. are mutually exclusive. Given the above definitions, from the eg in result.html 4. chr20-chr20 rf MCF7 SULF2 chr20 46415145 ENSG00000171940 chr20 52210297 22 18 27 MCF7 SULF2 chr20 46415146 ENSG00000171940 chr20 52210647 11 18 14 22 sets the limit on the number of reads spanning a fusion, why is the number 27 greater than 22? For 11. is it possible to give an illustration of what exactly you mean? I did the math by adding the genomic coordinate to the number and compared it to the coordinates in the reads section but the numbers do not match up. Also what is the difference between – and + number1 and number2 Really grateful if you can enlighten me! i have tried looking at the documentation but it is cryptic. i hope i am not sounding just at cryptic trying to put across concepts that require illustration.
 12-20-2012, 12:25 AM #2 mxqian Junior Member   Location: shanghai Join Date: Sep 2011 Posts: 3 I also want to get the answer!!!

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