Are you seeing this with any BED file, or just those where the chrom column is "1" rather than "chr1"? Column auto-detection for interval files looks for a name like chr, contig, scaffold, ... -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 22, 2013 at 4:35 PM, Anthonius deBoer <thondeboer@me.com> 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..
[image: Capture.JPG]
Here's a few lines from the file 13807695038077349 utr3:RSPO11- 38077349380773490,0,2551 3807742038078426 utr3:RSPO11 -3807842638078426 0,0,25513807842638078593 cds:RSPO11-38078426 38078593255,0,01 3807937538079564cds:RSPO11 -3807937538079564 255,0,01 3807985538080005 cds:RSPO11- 3807985538080005255,0,01 3808215538082347 cds:RSPO11 -3808215538082347 255,0,013809523938095333 cds:RSPO11- 38095239 38095333255,0,01 3809533338095621utr5:RSPO11 -3809562138095621 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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