How to remove X & Y chromosome genes from RNAseq data
0
Entering edit mode
Archit • 0
@Archit-24489
Last seen 5 days 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 • 128 views
ADD COMMENTlink
0
Entering edit mode
@mikelove
Last seen 2 days 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.

ADD COMMENTlink
0
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

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.

ADD REPLYlink
0
Entering edit mode

Thanks Michael

ADD REPLYlink
0
Entering edit mode

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.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.3