Entering edit mode
7.1 years ago
annen
▴
30
Does anyone have any info on the level of GC content disparity that is tolerable between samples? For example, if I have one group that has an average GC content of 41% (+/- 3) that I want to compare to one with an average GC content of 44% (+/- 2)- does this need to be accounted for in my analysis or is this considered equal? Any info is appreciated.
You've got bigger problems than GC content if you're trying to compare RNASeq between two different genomes. What is the experimental design?
Sorry, I guess I was unclear. They are samples from the same species, just two groups- a control group and a treated group. If I look at the reads from the control group, they have a GC content of 44% (+/- 2) compared to my treated group that is 41% (+/- 3). Is this within tolerance for looking at differential expression between treated and control or something that I need to account for?
That looks like a pretty big difference to me - which I wouldn't expect for a library between members of the same species. How many replicates do you have per group?
That's what I thought... I have 5 replicates per group.
Have you used the
cqnplot()function from the cqn package? That'd be more useful than comparing averages.I have not.. I will try that and see what it looks like. Thanks.