Total number of junctions in junctions.bed generated by TopHat
Hello, I run TopHat alignment on my RNA-Seq data and get some results within junctions.bed. This is an abstract that I want to understand for interpretations. I want to know the total number of junctions and the number of Found junctions and other explanations that go with it. Thanks lot.
track name=junctions description="TopHat junctions"
1 15010 15826 JUNC00000001 3 - 15010 15826 255,0,0 2 28,31 0,785
1 15920 16627 JUNC00000002 3 - 15920 16627 255,0,0 2 27,21 0,686
1 16735 16870 JUNC00000003 3 - 16735 16870 255,0,0 2 30,13 0,122
1 17020 17254 JUNC00000004 7 - 17020 17254 255,0,0 2 35,22 0,212
1 17346 17623 JUNC00000005 3 - 17346 17623 255,0,0 2 22,18 0,259
1 17723 17948 JUNC00000006 3 - 17723 17948 255,0,0 2 19,34 0,191
1 18027 18301 JUNC00000007 7 - 18027 18301 255,0,0 2 34,34 0,240
1 169237 172567 JUNC00000008 1 - 169237 172567 255,0,0 2 27,11 0,3319
1 185313 185524 JUNC00000009 5 - 185313 185524 255,0,0 2 37,34 0,177
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justinkablan225 •
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not sure if I understand but for the total number of junctions found you need to count the numbers of rows in that file (minus the header line ) .
I don't get what you mean by number of junctions vs found junctions ?
Check the materials and methods to see how they define "loaded" versus "found". If you want, provide such a manuscript.