Hi everyone,
I am looking at RNAseq data in IGV. I have colored the reads by insert size: https://ibb.co/mMwPKk
I am not sure what the dark-red/wine color represents. I looked at the documentation but couldn't find an explanation for this particular color. Is it the same as the red color they show in the docs? If so then it is possibly deletion. Can someone confirm if this represents deletion?
P.S.: All the reads (colored or otherwise) are on chr2.
Thanks!
Most probably it's one of the colours of chromosomes - see doc
You can easily check if the other pair of the respective reads fall on different chromosome, encoded by the above colour scheme
I should've mentioned in the question that I did check for it and all the reads are on chr2.
Just to be sure: did you check that the reads + their mate pairs are on chr2?
So I double checked and the mate pairs are on the same chromosome but the opposite strand. Is that what it is showing? If yes then can you please move your comment to an answer and I will accept it. Thanks!!
Nope. This is not what I was thinking. Let's wait for some more clarifications from others.