IGV RNAseq- Splice junction

Question

[vinishavvenugopal]

Hi,

I'm a beginner in RNAseq. Hope someone with expertise in IGV can clear this out for me.

What can I infer with a splice junction of depth 1 and how exactly is the flanking width related to this splice junction?

chr1:11022241-11023192 Strand: + Depth = 1, Flanking Widths: (30,95)

Answer 1

[xiaoleiusc]

chr1:11022241-11023192 means the coordinate of the intron position (chromosome 1, position 11022241-11023192), and Depth = 1 means only one alignment supports this splice junction. I do not know how to interpret the flanking widths.