Entering edit mode
2.8 years ago
Roy
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20
Hello all,
I am trying to clear up my confusion on interpreting this IGV:
From my knowledge and research, I would initially say that these red bars aren't too important since there are so many reads that do not contain these bars. However, the broad institute suggest this scattered red reads indicates possible deletions (https://software.broadinstitute.org/software/igv/interpreting_insert_size)
Should I assume this is a deletion even though there are plenty of reads that are considered normal?
Thanks
What do you mean by red bars?
Some reads are colored red based on a visualization choice that was made. What did you choose to color the reads as?
Then, when thinking about a deletion, walk your reasoning through the entire process. Where would the deletion be? Why would a red read indicate a deletion? What does "red" mean?
The red reads are by default deletions, but I don't understand your comment because you replied as a philosopher on the color red which is nothing to do with my question. I am asking that if maybe ten of my 100 reads have this deletion, why do the broadinstitute classify this as possible deletion? Should like 90% of the reads be red to be more confident in this? Where are these non-deleted reads coming from?
Thanks
I did perhaps sound like a philosopher, but that is because the question was a bit like that.
You need to understand what red means before you can interpret the reason why that implies a certain phenomenon.
The color red is most likely a characteristic of the alignment. Perhaps it indicates an unexpectedly large insert size, perhaps it indicates that it is an orphan read of a pair (the other side is missing).
Once you figure out why an alignment is colored red, then you can look for reasons that may lead to that characteristic.
Perhaps orphan reads indicate that the other pair comes from a region that does not exist in the reference, hence they "look orphan" because the current genome has a missing region compared to the originating genome.
The main point here is that the color "red" never directly means "deletion". It is red because the alignment has some sort of property that may or may not indicate a deletion.