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Old 01-12-2010, 09:55 PM   #1
Pepe
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Location: Germany

Join Date: Mar 2009
Posts: 28
Default TopHat coverage.wig file wish list

Hi,

I wanted to add to the list of things to have into account for the next version of TopHat, in case the developers are around.
I'm using Tophat v1.0.12 and Bowtie v0.11.3
I noticed that the last line for each chrm in the coverage.wig file ends a position earlier. For example, the last lines for scaffold1 in my coverage.wig file are:

scaffold1 4408480 4412926 0
scaffold1 4412926 4413006 1
scaffold1 4413006 4486297 0
scaffold1 4486297 4486376 1

I'm using 80 bp reads as you can see in the 2nd line pasted above (4413006-4412926=80), but the last line of the wig file shows a read of length 79 (4486376-4486297=79) (I've checked the SAM file and this read aligns in all 80 bases) I noticed that this happens on the last read/covered fragment of every chrm.

Do I get a price for helping make Tophat even a greater software than it'salready? If so, I would like to make one more wish.
All the chrms end on that last read/fragment aligned as opposed to have a last row with deph of coverage equal to 0 starting from the end of the last read/fragment and finishing at the end of the chrm.
In the example above scaffold1 is 4553411 nt long. A nice way to finish the chrm would be:
scaffold1 4486376 4553411 0

Finishing like this this will make the wig file complete and accurate, and will make it useful for coverage calculations, etc.

Thanks for developing a great software.
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Old 01-12-2010, 11:56 PM   #2
Xi Wang
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Location: MDC, Berlin, Germany

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Posts: 317
Default

I check my results. The same case.
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