Tophat junction.bed explanation

[emilyjia2000]

Hi,

I used Tophat to do mapping on RNA-seq data, it generated junction.bed, I know the first 4 column, the fifth column may be score, the six column is strand, but I don't know what means for the rest of columns. Please look at the output file:

track name=junctions description="TopHat junctions"
chr20 199813 204594 JUNC00000001 1 + 199813 204594 255,0,0 2 91,9 0,4772
chr20 199815 204700 JUNC00000002 85 - 199815 204700 255,0,0 2 93,92 0,4793
chr20 204652 205522 JUNC00000003 30 - 204652 205522 255,0,0 2 75,89 0,781

Please help me explain the rest of the columns. Do those columns represent some parameter setting in tophat?

THanks,

[kmcarr]

Here is the definition of the BED format at the UCSC browser site. Basically the additional colunms describe how the feature is displayed in the browser.

[emilyjia2000]

Thanks, I got it