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
13807695038077349utr3:RSPO11-38077349380773490,0,255
13807742038078426utr3:RSPO11-38078426380784260,0,255
13807842638078593cds:RSPO11-3807842638078593255,0,0
13807937538079564cds:RSPO11-3807937538079564255,0,0
13807985538080005cds:RSPO11-3807985538080005255,0,0
13808215538082347cds:RSPO11-3808215538082347255,0,0
13809523938095333cds:RSPO11-3809523938095333255,0,0
13809533338095621utr5:RSPO11-38095621380956210,0,255

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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