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We are using TopHat fusion for two data sets we have and there is something not clear to me in the output:
The last three columns are :
- Number of spanning reads - I understand that those are split reads
-Number of spanning mate pairs - I understand that these are pairs for which one is 5' to the breakpoint and one is 3' to the breakpoint
-Number of spanning mate pairs where one end spans a fusion - here we do not understand what is the difference from the first column ("Number of spanning reads").
I also saw that the R package Chimera use only this last column for filtration - were I would intuitively use also (or solely) the first two - so is there a special importance to this last column ?
One last question - is there a practical criteria for which to filter the fusion results?
The last three columns are :
- Number of spanning reads - I understand that those are split reads
-Number of spanning mate pairs - I understand that these are pairs for which one is 5' to the breakpoint and one is 3' to the breakpoint
-Number of spanning mate pairs where one end spans a fusion - here we do not understand what is the difference from the first column ("Number of spanning reads").
I also saw that the R package Chimera use only this last column for filtration - were I would intuitively use also (or solely) the first two - so is there a special importance to this last column ?
One last question - is there a practical criteria for which to filter the fusion results?