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 <thondeb...@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 > > ___________________________________________________________ > 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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