Hi,

I have installed local galaxy. I used the Tophat to do the RNA-seq alignment and got a output file: splice junction in bed format.

I can not understand it clearly. What does the number 17, 14 ... in the column 5 mean ? What does the 87,93 mean ? What does the 0, 4787 mean ? Can you explain a little bit to me ? Which tool can be used to view this file ?

Thanks,  

track name=junctions description="TopHat junctions"
chr20      199821     204701     JUNC00000001     17        -        199821      204701      255,0,0     2        87,93     0,4787
chr20      204631     205520     JUNC00000002     14        -        204631      205520      255,0,0     2        96,87     0,802
chr20      205428     205775     JUNC00000003      9        -        205428      205775      255,0,0     2        92,91     0,256
chr20      205699     205958     JUNC00000004     15        -        205699      205958      255,0,0     2        87,92     0,167
chr20      205929     207067     JUNC00000005     31        -        205929       207067     255,0,0     2        95,97     0,1041
chr20      206977     207909     JUNC00000006     19        -        206977       207909     255,0,0     2        93,97     0,835
chr20      207884     212679     JUNC00000007     15        -        207884        212679    255,0,0     2        87,76     0,4719
chr20      207910     218238     JUNC00000008      1        -        207910        218238    255,0,0     2        61,39     0,10289
chr20       212628    218293     JUNC00000009     28        -        212628        218293    255,0,0     2        94,94     0,5571


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