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Old 01-15-2010, 08:35 PM   #1
Gangcai
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Question Problem for tophat coverage.wig files

Hi everyone, I have meet a problem for coverage.wig:

chr1 11358 11434 1
chr1 11434 11583 0
chr1 11583 11659 1
chr1 11659 11871 0

my reads length is 76,
for "chr1 11358 11434 1"
11434-11358=76, and the coverage is 1
But the problem is which part is included for this coverage, 11434(start) or 11358(end) ? (the coverage for 11434 is 1 or 0?)
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Old 01-15-2010, 08:47 PM   #2
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From the UCSC browser, it seems only the end is included, which means the reads coverage for 11434 is 1.
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Old 01-16-2010, 05:14 AM   #3
Xi Wang
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the definiation of four col BED format is:

Bedgraph track data values can be integer or real, positive or negative values. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data must be in numerical order. The bedGraph format has four columns of data:
chrom chromStart chromEnd dataValue
Note: These coordinates are zero-based, half-open.

refer to: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
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Old 01-16-2010, 06:43 PM   #4
Gangcai
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Thanks for your reply!
So this means for 0-base chromosome postion, the start part is included. But for 1-based chromosome position, the end part is included(Just treat as 1-based).
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Old 01-16-2010, 06:56 PM   #5
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But for 1-based, the start position is not included. The interval length is exactly END-START
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