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tophat: definition of spanning mate pair
I have found a reference where the "encompassing" read and "spanning" reads are being clearly distinguished and well defined.
"Encompassing mate pairs refer to those in which
each read aligns to an independent transcript, thereby encompassing
the fusion junction. Spanning mate pairs refer to those in
which one sequence read aligns to a gene and its mate spans the
fusion junction."
However, using tophat has been very confusing with no clear definition or figures to explain the wording.
On tophat webpage, three types of reads are mentioned:
"1. 106 is the number of reads that span the fusion,
2. 116 is the number of mate pairs that support the fusion,
3. 167 is the number of mate pairs that support the fusion and whose one end spans the fusion."
Which one of the last two statements refer to encompassing and spanning mate pairs? Which out of 2 and 3 carries more weight? Any thoughts?
"Encompassing mate pairs refer to those in which
each read aligns to an independent transcript, thereby encompassing
the fusion junction. Spanning mate pairs refer to those in
which one sequence read aligns to a gene and its mate spans the
fusion junction."
However, using tophat has been very confusing with no clear definition or figures to explain the wording.
On tophat webpage, three types of reads are mentioned:
"1. 106 is the number of reads that span the fusion,
2. 116 is the number of mate pairs that support the fusion,
3. 167 is the number of mate pairs that support the fusion and whose one end spans the fusion."
Which one of the last two statements refer to encompassing and spanning mate pairs? Which out of 2 and 3 carries more weight? Any thoughts?