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
Yep you're pretty much there.
Assuming counts is your counts matrix containing all samples, something to the effect of:
subset <- counts[which(rownames(counts) != biomart_list$Gene),]
edit: != must be dataframes of equal length
Hi Barry, I am getting a warning "Warning message: In rownames(countdata) != X_Y$Geneid : longer object length is not a multiple of shorter object length".
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. .
Hi Barry, sorry for delay in replying. I tried !(rownames(countdata) %in% X_Y$Geneid).
I am not getting any error but it is also not removing Geneid.
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archit22684 •
> head(rownames(countdata))
[1] "ENSG00000223972" "ENSG00000227232" "ENSG00000278267" "ENSG00000243485" "ENSG00000284332"
[6] "ENSG00000237613"
> head(X_Y$Geneid)
[1] "ENSG00000228572" "ENSG00000182378" "ENSG00000178605" "ENSG00000226179" "ENSG00000167393"
[6] "ENSG00000281849"
head(rownames(countdata)) [1] "ENSG00000223972" "ENSG00000227232" "ENSG00000278267" "ENSG00000243485" "ENSG00000284332" [6] "ENSG00000237613" head(X_Y$Geneid) [1] "ENSG00000228572" "ENSG00000182378" "ENSG00000178605" "ENSG00000226179" "ENSG00000167393" [6] "ENSG00000281849"
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Hi Barry, I am getting a warning "Warning message: In rownames(countdata) != X_Y$Geneid : longer object length is not a multiple of shorter object length".