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Old 02-28-2012, 06:50 PM   #2
Alex124
Junior Member
 
Location: Melbourne

Join Date: Feb 2012
Posts: 2
Default Explanation of junctions.bed

[seqname] [start] [end] [id] [score] [strand] [thickStart] [thickEnd] [r,g,b] [block_count] [block_sizes] [block_locations]
"start" is the start position of the leftmost read that contains the junction.
"end" is the end position of the rightmost read that contains the junction.
"id" is the junctions id, e.g. JUNC0001
"score" is the number of reads that contain the junction.
"strand" is either + or -.
"thickStart" and "thickEnd" don't seem to have any effect on display for a junctions track. TopHat sets them as equal to start and end respectively.
"r","g" and "b" are the red, green, and blue values. They affect the colour of the display.
"block_count", "block_sizes" and "block_locations":
The block_count will always be 2. The two blocks specify the regions on either side of the junction. "block_sizes" tells you how large each region is, and "block_locations" tells you, relative to the "start" being 0, where the two blocks occur. Therefore, the first block_location will always be zero.

[read_start][junction][read_end]
[block1 ][ ][block2]
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