Entering edit mode
6.2 years ago
statfa
▴
760
Hi guys,
I was hoping here that if one sample is sequenced in each lane, I don't need to correct gc content bias. But now that I don't know how to find number of samples in each lane, I wanna check if GC content bias has occurred. Should I use deep tools (computeGCBias) on galaxy for my rna-seq bam files and then deep tools (correctGCBias) to correct the bias? There are some statistical methods to correct GC bias in table of read counts too. Which one is better? using deep tools on bam files or using other methods available for counts table? I want to do differential expression analysis.
Thank you
Multiple questions with similar question content (Number of samples in each lane in GEO datasets ) is not always fruitful.If you feel strongly about looking for and correcting GC bias then by all means go for it. You may have to try multiple methods to see what works best for the data you have.
It's a different question. There I asked how to find the number of samples in each lane. Nobody knew that. @Devon said if I feel a need to check the bias, then I can do that but he didn't say how. Now I'm asking how. What tools? I searched not only on biostars but on google too. What I learned was to use deep tools. But I still have those questions that I have asked above.
Fair enough. I assume you have already used CQN (which was what you had used in past thread). Now you have found a couple of tools from deepTools and are following-up.
Well, actually, @Devon told me to normalize the data by CQN package. But in fact, we should make sure, first, that there is any bias. I wanna know if I'm right about deep tools detecting the GC-content bias. Then, if I find any bias, removing GC-content bias in bam files using deep tools is better or normalizing the bias in counts table using methods like CQN package?
I am not familiar with CQN. Perhaps deepTools is using CQN like method under cover to do the correction. I will tag @Devon on this post so he can comment.
Thank you very much genomax. I'll appreciate it. Sorry if I bother a lot.
No bother at all. I learn new things here everyday.
And I'm not dumb ;-) I know my posts are available even if I change my username. I changed it because of some other reasons. Don't be so pessimistic. If you look at each of my threads, You will see there are big differences in them ;-)
Tagging: Devon Ryan