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..

<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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