Hello everyone, I am new in this field. I have used STAR and featurecounts followed by DEse2 for my RNAseq analysis. I want to remove X and Y chromosome genes from my bulk seq data. I don't know how to proceed with that. Do I need to remove the genes from the counts after featurecounts or using the Deseq2? I have made a list of X&Y chromosomes Gene_id using Biomart. Can I remove the Gene_id's of X and Y chromosomes from my count data? Will this be the correct way of doing it? Any help is appreciated. Thanks
Hi Barry, I am getting a warning "Warning message: In rownames(countdata) != X_Y$Geneid : longer object length is not a multiple of shorter object length".
!(rownames(counts) %in% X_Y$Geneid). I don't see how
!=would work comparing 2 vectors of incompatible sizes.
My bad, I'm used to biomaRt df's derived from count rownames. Feel free to change yours to an answer and ill remove mine. .
Don't worry about that. If it works somewhere, that is knowledge worth sharing. Maybe just add a note stating where
!=works and where it doesn't.
Hi Barry, sorry for delay in replying. I tried
!(rownames(countdata) %in% X_Y$Geneid). I am not getting any error but it is also not removing Geneid.
What is the output to:
Well they do look similar and should ideally overlap. Can you get some help from someone in your team/institution? This needs more involved help but should not take more than a few minutes to figure out.