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Hi, 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 also tried using the code from the previous post (https://support.bioconductor.org/p/67237/) for subsetting the data but I think that is not removing the genes. The code is working fine and I am not getting any error in that. I think is am not using it correctly for removing Xand Y chromosome genes. Any help is appreciated. Thanks
dds[ all(!seqnames(dds) %in% c("chrX", "chrY")), ]
Thanks Michael for your response. I am new in this field. I have made a list of X&Y chromosomes Gene_id using Biomart. Can't I just remove the Gene_id of X and Y chromosomes from my countdata? Will this be the correct way or I need to go through featurecounts only? Thanks
This is outside the scope of what I can provide as the DESeq2 developer. I can't provide general bioinformatics help to all comers, but reserve my time for support related to the DESeq2 software.
For general bioinformatics help you can post instead to biostars.
Thanks Michael
I'm sorry to bump this old thread, but did you ever find a solution? I have .txt output files from featureCounts that I need to remove the genes from the x and y chromosome. I'd message you directly, but my it's preventing me from doing so for some reason.
Please don't bump a thread and apologize for doing so. Instead, don't bump the thread but start a new one. You can always refer to the old thread.
Thank you. I will stick to this etiquette from now on.
I think this should work fine. Get a list of ENSEMBL IDs for genes in X and Y chromosomes (say from biomaRt), run a loop through each line of the dds object, and make a list of the indices which contain ENSEMBL IDs matching with your list ( of X and Y ID's). Simply subset your dds object (remove the lines containing those indices) and proceed with DESeq2 analysis. Hope this helps.