IGV read color ,what is inferred insert size and expected insert size mean?
0
0
Entering edit mode
6 weeks 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? enter image description here

IGV • 369 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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 enter image description here

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6