How to remove X & Y chromosome genes from RNAseq data
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Archit • 0
@Archit-24489
Last seen 6 months ago

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")), ]
DESeq2 RNASeq • 248 views
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@mikelove
Last seen 7 hours ago
United States

You will need to identify the genes associated with those chromosomes. If you've used featureCounts, check their manual on where that information is stored.

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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

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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.

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Thanks Michael

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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.

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