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6 months ago
Tao
▴
40
why this read pair is red in IGV?
I see the IGV doc,read pair marked in red means inferred insert size will be larger than expected, How to calculate the expected insert size and inferred insert size?
See the illustration here : What is the difference between a Read and a Fragment in RNA-seq?
Insert size is calculated based on the alignment of the two reads to the reference genome.
I understand how insert size and fragment length are calculated, but I don't know inferred insert size and expected insert size. Inferred insert size larger than expected will be marked in red,but how to know it should be red.
![enter image description here](/media/images/0fdcdce8-58ec-438e-b3f7-3674be51)
Not sure what you mean by "how to know it should be red"? That is the color scheme IGV is using based as noted in the shot you posted above.