I used TopHat to find exon-exon junctions.
But the results in the output 'junctions.bed' files confused me.
I seperated RNA-seq data into two datasets as one is 76bp*2 another is 40bp*2, then ran TopHat individually.
However, the two 'junctions.bed' files gave different results.
Here are examples of the two 'junctions.bed' result:
One reports the following junctions:
chromosome12 12302 12721 JUNC00000002 5 -
chromosome12 33389 34997 JUNC00000003 6 +
chromosome12 33688 34964 JUNC00000004 2 +
chromosome12 35474 35675 JUNC00000005 5 +
chromosome12 35718 35949 JUNC00000006 9 +
Another reports the following junctions:
chromosome12 12303 12723 JUNC00000005 26 -
chromosome12 33679 34982 JUNC00000007 3 +
chromosome12 35490 35674 JUNC00000008 6 +
chromosome12 35711 35949 JUNC00000009 7 +
These junction locations of each output file were similar but different.
When I extracted the detailed sequences, no GT-AG was found.
Does anybody know how to explain it?
But the results in the output 'junctions.bed' files confused me.
I seperated RNA-seq data into two datasets as one is 76bp*2 another is 40bp*2, then ran TopHat individually.
However, the two 'junctions.bed' files gave different results.
Here are examples of the two 'junctions.bed' result:
One reports the following junctions:
chromosome12 12302 12721 JUNC00000002 5 -
chromosome12 33389 34997 JUNC00000003 6 +
chromosome12 33688 34964 JUNC00000004 2 +
chromosome12 35474 35675 JUNC00000005 5 +
chromosome12 35718 35949 JUNC00000006 9 +
Another reports the following junctions:
chromosome12 12303 12723 JUNC00000005 26 -
chromosome12 33679 34982 JUNC00000007 3 +
chromosome12 35490 35674 JUNC00000008 6 +
chromosome12 35711 35949 JUNC00000009 7 +
These junction locations of each output file were similar but different.
When I extracted the detailed sequences, no GT-AG was found.
Does anybody know how to explain it?
Comment