BEDPE format and UCSC Genome Browser

[Jim]

Aaron,
Nice work on the BEDTools, It's very useful. I downloaded today and
wanted to view a PE dataset in UCSC Browser and I've found that the
BEDPE format doesn't seem to match the expected input. Can you shed
light on what I'm doing wrong?

chr2 18814828 18814867 chr2 18814996
18815035 unknown_0001:7:49:3166:16929#0 255 + -
chr2 18814842 18814881 chr2 18814994
18815033 unknown_0001:7:90:9361:19316#0 255 + -
chr2 18814855 18814894 chr2 18815049
18815088 unknown_0001:7:69:4021:7269#0 255 + -

Thanks,

Jim

[Aaron Quinlan]

Hi Jim,
BEDPE is a custom format defined for BEDTools and does not work directly on the browser. We needed something beyond BED12 (aka blocked BED) because BED12 only allows one strand and one chromosome to be specified. Therefore, one cannot represent trans-chromosomal events such as fusion genes, reciprocal translocations or transposon insertions. That said, clearly a limitation of BEDPE is that it cannot be displayed on the browser.

Somewhere in my source tree I have a Python script that will convert BEDPE to BED12, but it only works for intra-chromosomal BEDPE features. Would you be interested in this? Would others? If so, I can post it to the BEDTools site and eventually add it to future releases. Note that it is experimental...

Best,
Aaron

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[Wei Tang]

yes please post to the BEDTools, we need it.

[Aaron Quinlan]

I'll post this script tonight or tomorrow.

Aaron