I am dealing with RNA seq data and i am using different softwares for detection of splicing events.
I came across hmmsplicer tool. I have a question in it. It generates 2 main files namely junctions.final.bed and junctions.noncanonical.bed.
The 5th column is the score column in the bed file. This column actually tells us the depth of that junction meaning how many reads actually span the junction. The score here includes decimal points. Now my question is that is it ok to have score/depth in decimals because tophat gives integer values and not decimals.
Moreover in 4th column sometimes i find SRR036966.9097539|junc=3 . Now wat is the significance or meaning of junc=3.
There are many cases like
Hope to hear from you guys soon