Hi Thon We see the same with our BED files, and I can reproduce it with your example. I tend to ignore it since (so far) it has no influence on the functionality, if I use the BED file in any other tool. I only run into troubles when I present working with BED files in our introductory courses.... Sorry, no solution. Regards, Hans-Rudolf On 01/22/2013 10:35 PM, Anthonius deBoer wrote:
Hi,
I have noticed for a while now that BED files are not recognized correctly or at least not parsed out correctly. I notice that invariably, the (9 column) BED file comments state there is 1 region and X comments, where X + 1 is the actual number of regions in the file..
Capture.JPG
Here's a few lines from the file 1 38076950 38077349 utr3:RSPO1 1 - 38077349 38077349 0,0,255 1 38077420 38078426 utr3:RSPO1 1 - 38078426 38078426 0,0,255 1 38078426 38078593 cds:RSPO1 1 - 38078426 38078593 255,0,0 1 38079375 38079564 cds:RSPO1 1 - 38079375 38079564 255,0,0 1 38079855 38080005 cds:RSPO1 1 - 38079855 38080005 255,0,0 1 38082155 38082347 cds:RSPO1 1 - 38082155 38082347 255,0,0 1 38095239 38095333 cds:RSPO1 1 - 38095239 38095333 255,0,0 1 38095333 38095621 utr5:RSPO1 1 - 38095621 38095621 0,0,255
Any ideas why it thinks there are comments in the file and why only one region?
The file is a regular txt file without the LF and is not DOS format or anything...
It also does not parse out the name, score and strand info, but once I correct that manually, it works, but it is a pain to have to do that everytime...
Thanks,
Thon
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