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Old 04-05-2011, 01:16 PM   #1
gsinghal
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Location: St Louis, Missouri, USA

Join Date: Jul 2010
Posts: 2
Default How to make sense of Tophat's output file 'junctions.bed'

This is an excerpt from junctions.bed, Tophat's output file generated using paired-end reads. Can somebody suggest how to make sense of the two bed blocks? Both bed blocks have the same coordinates. Besides, how to infer the scores (apparently, which represent the number of alignments spanning the junctions)


chr20 9353709 9360718 JUNC00000552 2 + 9353709 9360718 255,0,0 2 42,18 0,6991
chr20 9365023 9368124 JUNC00000553 1 + 9365023 9368124 255,0,0 2 35,15 0,3086
chr20 9368172 9370544 JUNC00000554 2 + 9368172 9370544 255,0,0 2 31,19 0,2353
chr20 9371222 9374262 JUNC00000555 7 + 9371222 9374262 255,0,0 2 40,28 0,3012
chr20 9374285 9376179 JUNC00000556 1 + 9374285 9376179 255,0,0 2 40,10 0,1884
chr20 9376224 9382178 JUNC00000557 5 + 9376224 9382178 255,0,0 2 41,42 0,5912
chr20 9385955 9388573 JUNC00000558 1 + 9385955 9388573 255,0,0 2 40,10 0,2608
chr20 9388666 9389312 JUNC00000559 4 + 9388666 9389312 255,0,0 2 39,33 0,613
chr20 9389328 9389741 JUNC00000560 6 + 9389328 9389741 255,0,0 2 36,38 0,375
chr20 9389783 9391703 JUNC00000561 3 + 9389783 9391703 255,0,0 2 45,20 0,1900
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Gaurav Singhal
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