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 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).