One way we dealt with this discrepancy between chromosome nomenclature, in the commercial software Avadis NGS (for which I was a Product Manager some time ago, so full disclosure there) was to instigate what we called aliases for the chromosomes... A build could have multiple ways to refer to a chromosome and we simply had an alias table we consulted for the build we were using... This was very useful to know that "1", "chr1" and "chr1.fa" (Thanks Illumina) were all refering to the same chromosome... it made life SO much easier to deal with all these different ways of analysis...
We already have to make the build.txt file (and produce the .len files as well, I noticed all of a sudden), so we should be able to use ALIASES as I described pretty easilyl...
Thon
On Jan 24, 2013, at 07:31 AM, James Taylor james@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, ...
-- 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..
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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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