Hi Julie,
Refer to the BED format
(http://genome.ucsc.edu/FAQ/FAQformat.html#format1) and take a look at
columns 2,3,8,11, and 12 of your example. Your first entry, line two of
the custom track has:
chromStart chromEnd thickEnd blockSizes blockStarts
100026040 100026515 100026515 100,100 0,475
If you look, the second block starts at 475 (which is relative to
chromStart) and it's size is 100. That means that this block will end
well past chromEnd of 100026515 . In fact, it looks like your chromEnd
is set to where the second block should start. Or rather... your second
block starts 475 past chromStart, so 100026040 + 475 = 100026515. And
the second block size is 100, so 100026515 + 100 = 100026615. If you
set your chromEnd (and thickEnd!) to be 100026615 it will load fine.
E.g., line 2 (your first entry) should look like:
chr10 100026040 100026615 HWUSI-EAS1643R:12:FC:2:26:14731:4761
0 + 100026040 100026615 190,190,190 2 100,100
0,475
It looks like you have this same issue on every line.
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 2/27/12 7:32 AM, Sibbring, Julie wrote:
> Hello,
>
> I'm trying to load a BED file but I get the following error message:
>
> Error File
> 'ID713_2A.ID713_2M.map.ab.sam.all.links.filtered.compared.T2_2Av2M_mini.bed.txt'
> - Error line 2 of custom track: BED chromStarts[i]+chromStart must be less
> than chromEnd.
>
> As far as I can see, the numbers on column 2, chromStart, are less than
> column 3, chromEnd - see below.
>
> track
> name="/pub9/julie/ID713_fam002/svdetect/ID713_2A.ID713_2M.map.ab.sam.all.links.filtered.compared.bed.txt"
> description="mate pairs involved in links" visibility=2 itemRgb="On"
> chr10 100026040 100026515 HWUSI-EAS1643R:12:FC:2:26:14731:4761
> 0 + 100026040 100026515 190,190,190 2
> 100,100 0,475
> chr10 100026703 100026869 HWUSI-EAS1643R:12:FC:2:11:4081:14654
> 0 + 100026703 100026869 190,190,190 2
> 100,100 0,166
> chr10 100026158 100026610 HWUSI-EAS1643R:12:FC:4:73:16621:16526
> 0 + 100026158 100026610 0,0,0 2 100,100
> 0,452
> chr10 100026407 100026841 HWUSI-EAS1643R:12:FC:4:106:16094:2084
> 0 + 100026407 100026841 0,0,0 2 100,100
> 0,434
> chr10 100026624 100027013 HWUSI-EAS1643R:12:FC:4:22:12769:10441
> 0 + 100026624 100027013 0,0,0 2 100,100
> 0,389
>
> I would be grateful for any suggestions.
>
> Thank you,
>
> Julie
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
