How to interpret the bed file results from TopHat?

[zach]

I have some naive question in terms of the output from TopHat. Need your help.

track name=junctions description="TopHat junctions"
chr start end name score strand thickst thickend xxx blockcount blocksize
test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170
test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151


Question: 1) what kind of score (here 46 and 38) is a good indicative of splicing junction
2) the block count is the read counts on the two sides of a junction? e.g. 70, 52 means 70 reads on the left and 52 reads on the right of the junction
3) what is the first number 0 in the block size 0,170. In this case I assume that the block size is 170 nt. And therefore the gap (intron) between this junction is 52 based on the calculation 402 - 180 = 222 and then 222 -170 = 52.

[brentp]

that's bed format. check here: http://genome.ucsc.edu/FAQ/FAQformat#format1
the last 2 columns are blockSizes and blockStarts
where block starts are relative ot the start column.

[frymor]

I know it is a long shot, but maybe someone is following... :-)

I still don't understand how tophat calculate the last two columns.

this is what I have:

track name=junctions description="TopHat junctions"
2L      11489   11856   JUNC00000001    6       -       11489   11856   255,0,0 2       29,78   0,289
2L      12168   12323   JUNC00000002    1       -       12168   12323   255,0,0 2       53,38   0,117
2L      12864   13603   JUNC00000003    34      -       12864   13603   255,0,0 2       64,84   0,655
2L      13538   13764   JUNC00000004    37      -       13538   13764   255,0,0 2       87,82   0,144
2L      17136   18331   JUNC00000005    5       -       17136   18331   255,0,0 2       76,71   0,1124
2L      17136   21136   JUNC00000006    5       -       17136   21136   255,0,0 2       76,71   0,3929
2L      26888   27124   JUNC00000007    6       -       26888   27124   255,0,0 2       76,72   0,164
2L      28838   29069   JUNC00000008    11      -       28838   29069   255,0,0 2       88,88   0,143
2L      34259   34604   JUNC00000009    2       -       34259   34604   255,0,0 2       29,47   0,298

I don't understand how the blockLocation and blockSizes are calculated. Are this arbitrary numbers?

Assa