IGV read color ,what is inferred insert size and expected insert size mean?
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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.
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.