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Hi,
I know it has been discussed here a few times, but no one really explain how it is done.
I have this example of a tophat junction.bed file:
I understand what it means in general. What I would like to know is how it is calculated.
Here is what I understand:
the last three columns determine how many blocks each bed segment will have. the third column from the end is always 2, as there are two blocks.
the column before last gives the block sizes. this means how many base positions each block is taking in the browser (IGV, UCSC etc.). the last columns gives the length of the connection between the two blocks.
as an example of the calculations - row 1:
length of segment - 11856 - 11489 = 367 bases
block1: start position 0 (relative) and has the length of 29 positions.
block2: start at position 289-78 = 211 and has the length 78 positions.
this is how it looks like in the browser:
What I don't get is how these numbers are being calculated.
Why tophat says the first block is 29 bases long and the second one 78 bases. What are these numbers?
thanks for the help
Assa
I know it has been discussed here a few times, but no one really explain how it is done.
I have this example of a tophat junction.bed file:
Code:
chr2L 11489 11856 JUNC00000001 6 - 11489 11856 255,0,0 2 29,78 0,289 chr2L 12168 12323 JUNC00000002 1 - 12168 12323 255,0,0 2 53,38 0,117 chr2L 12864 13603 JUNC00000003 34 - 12864 13603 255,0,0 2 64,84 0,655 chr2L 13538 13764 JUNC00000004 37 - 13538 13764 255,0,0 2 87,82 0,144 chr2L 17136 18331 JUNC00000005 5 - 17136 18331 255,0,0 2 76,71 0,1124 chr2L 17136 21136 JUNC00000006 5 - 17136 21136 255,0,0 2 76,71 0,3929 chr2L 26888 27124 JUNC00000007 6 - 26888 27124 255,0,0 2 76,72 0,164 chr2L 28838 29069 JUNC00000008 11 - 28838 29069 255,0,0 2 88,88 0,143 chr2L 34259 34604 JUNC00000009 2 - 34259 34604 255,0,0 2 29,47 0,298
Here is what I understand:
the last three columns determine how many blocks each bed segment will have. the third column from the end is always 2, as there are two blocks.
the column before last gives the block sizes. this means how many base positions each block is taking in the browser (IGV, UCSC etc.). the last columns gives the length of the connection between the two blocks.
as an example of the calculations - row 1:
length of segment - 11856 - 11489 = 367 bases
block1: start position 0 (relative) and has the length of 29 positions.
block2: start at position 289-78 = 211 and has the length 78 positions.
this is how it looks like in the browser:
What I don't get is how these numbers are being calculated.
Why tophat says the first block is 29 bases long and the second one 78 bases. What are these numbers?
thanks for the help
Assa