Hi,
I have run with tophat2 for many samples seperately and got junctions.bed files. When I combined all the junctions.bed file together to get the information of junction boundary and coverage score, I found the boundary between samples fluctuate with 1-3bp very often. Here are examples:
The header of these columns are: scaffoldID start end junctionID score strand. the scores were set to 0.
I checked manually for different samples found that different samples have different boundary.
I have run with tophat2 for many samples seperately and got junctions.bed files. When I combined all the junctions.bed file together to get the information of junction boundary and coverage score, I found the boundary between samples fluctuate with 1-3bp very often. Here are examples:
Code:
C189205324 196 484 JUNC0001692 0 - C189205324 199 770 JUNC0001693 0 - C189205324 203 775 JUNC0001694 0 - C189205324 206 770 JUNC0001695 0 - C189205324 210 771 JUNC0001696 0 - C189205324 213 772 JUNC0001697 0 - C189205324 219 774 JUNC0001698 0 - C189205324 220 775 JUNC0001699 0 - C189205324 220 804 JUNC0001700 0 - C189205324 470 787 JUNC0001701 0 - C189205324 470 817 JUNC0001702 0 - C189205324 470 818 JUNC0001703 0 - C189205324 470 821 JUNC0001704 0 - C189205324 470 823 JUNC0001705 0 - C189205324 470 824 JUNC0001706 0 - C189205324 470 827 JUNC0001707 0 - C189205324 470 830 JUNC0001708 0 - C189205324 474 784 JUNC0001709 0 - C189205324 478 782 JUNC0001710 0 - C189205324 490 777 JUNC0001711 0 - C189205324 490 779 JUNC0001712 0 - C189205324 490 782 JUNC0001713 0 - C189205324 490 787 JUNC0001714 0 - C189205324 490 798 JUNC0001715 0 - C189205324 492 774 JUNC0001716 0 - C189205324 492 775 JUNC0001717 0 - C189205324 496 775 JUNC0001718 0 - C189205324 497 775 JUNC0001719 0 - C189205324 499 795 JUNC0001720 0 - C189205324 500 785 JUNC0001721 0 - C189205324 501 797 JUNC0001722 0 - C189205324 851 1028 JUNC0001723 0 -
I checked manually for different samples found that different samples have different boundary.
Comment