Well...I guess it should not be forcing us to use the chr1 notation, especially since the decoy hg19 genome I am using is not using that convention...This is the age old problem with the two ways of refering to the position on the genome...What i call the UCSC way and the "other" way, such as BROAD is using for their decoy genome...
Any way we can make those interval parser a little "wiser" about other ways to refer to a contig/chromosome?
Thanks,
Thon
On Jan 24, 2013, at 07:31 AM, James Taylor <ja...@jamestaylor.org> wrote:
On Jan 24, 2013, at 07:31 AM, James Taylor <ja...@jamestaylor.org> wrote:
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, ...
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James Taylor, Assistant Professor, Biology/CS, Emory UniversityOn 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..<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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