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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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