STAR vs TopHat viewing junctions

[biocomputer]

STAR and TopHat both output a file indicating junctions. The TopHat version is a 12-column .bed file generally indicating exons while the STAR version is somewhat proprietary format with the first 3 columns (chrom, start, end) indicating introns.



I find the TopHat version more visually useful. Is there any way to convert the STAR output into something like TopHat shows?

[dpryan]

You should be able to use awk to convert one format to the other, since it's just a matter of adding some columns and doing some simple arithmetic. Just look at one of the lines in the tophat file and the corresponding one in the STAR file and it should be obvious how to convert them.