IGV color interpretation by insert size

Question

[komal.rathi]

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!

[Santosh Anand]

Most probably it's one of the colours of chromosomes - see doc

for paired end reads that are coded by the chromosome on which their mates can be found

You can easily check if the other pair of the respective reads fall on different chromosome, encoded by the above colour scheme

[komal.rathi]

I should've mentioned in the question that I did check for it and all the reads are on chr2.

[Santosh Anand]

Just to be sure: did you check that the reads + their mate pairs are on chr2?

[komal.rathi]

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!!

[Santosh Anand]

Nope. This is not what I was thinking. Let's wait for some more clarifications from others.

Answer 1

[Istvan Albert]

When it comes to IGV some of the colors are not explained well. In addition, these colors may occasionally change slightly.

You kind of get their interpretation of them by trial - most likely means that the distance between paired reads is much larger/smaller than the expected distances computed from other reads.

View also as pairs and hover over a few of the colored pairs. There are not that many things to look for. Distance, orientation, different chromosomal matches.