I apologize if this has been answered somewhere else.
I'm trying to do some analysis on a dataset at http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1023125 published as a BED file.
Unfortunately, the "BED" file is in a bit of a weird format, which looks like semi-processed Bowtie output:
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.
I'm trying to do some analysis on a dataset at http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1023125 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 +
Any pointers would be greatly appreciated.