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Old 03-06-2013, 11:06 AM   #1
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Default Converting contig coordinates to genomic coordinates

I apologize if this has been answered somewhere else.

I'm trying to do some analysis on a dataset at published as a BED file.

Unfortunately, the "BED" file is in a bit of a weird format, which looks like semi-processed Bowtie output:

HTML Code:
gi|149288852|ref|NC_000067.5|NC_000067	176269827	176269871	HWI-ST363:283:C0ND8ACXX:8:1101:2034:2233	255	-
gi|149288852|ref|NC_000067.5|NC_000067	154993040	154993084	HWI-ST363:283:C0ND8ACXX:8:1101:3639:2182	255	+
gi|149338249|ref|NC_000068.6|NC_000068	155564443	155564487	HWI-ST363:283:C0ND8ACXX:8:1101:3703:2191	255	-
gi|149354223|ref|NC_000070.5|NC_000070	42195036	42195080	HWI-ST363:283:C0ND8ACXX:8:1101:5142:2130	255	-
gi|149292731|ref|NC_000078.5|NC_000078	79949131	79949175	HWI-ST363:283:C0ND8ACXX:8:1101:5103:2145	255	+
The coordinates are given as contigs (plus gi numbers, which i can easily strip off) instead of genomic coordinates. I've read around and UCSC genome browser used to support contigs in BED files, but they no longer do. There are also several references to the liftUp tool that converts contigs to genome coordinates, but I can no longer locate any place to download liftUp or its source code. So before I venture into re-writing liftUp, I was wondering if there is another tool that I could use (or maybe a place to download liftUp).

Any pointers would be greatly appreciated.
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