Question: GC bias between samples tolerance in RNAseq?
0
gravatar for annen
16 months ago by
annen30
annen30 wrote:

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.

rna-seq bias gc • 482 views
ADD COMMENTlink written 16 months ago by annen30

You've got bigger problems than GC content if you're trying to compare RNASeq between two different genomes. What is the experimental design?

ADD REPLYlink written 16 months ago by karl.stamm3.4k

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?

ADD REPLYlink written 16 months ago by annen30

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?

ADD REPLYlink written 16 months ago by WouterDeCoster37k

That's what I thought... I have 5 replicates per group.

ADD REPLYlink written 16 months ago by annen30

Have you used the cqnplot() function from the cqn package? That'd be more useful than comparing averages.

ADD REPLYlink written 16 months ago by Devon Ryan88k

I have not.. I will try that and see what it looks like. Thanks.

ADD REPLYlink written 16 months ago by annen30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 752 users visited in the last hour