Question: How to create manhattan plot with DESeq2
0
gravatar for adeler001
29 days ago by
adeler0010
adeler0010 wrote:

I used DESeq2 to do my Differential gene expression analysis for my RNA seq data. I would like to know what script I can use to generate a manhattan plot where I have the chromosome position on the x axis and p values on the y axis .

Thanks

ADD COMMENTlink modified 29 days ago by Michael Love26k • written 29 days ago by adeler0010
Answer: How to create manhattan plot with DESeq2
0
gravatar for Michael Love
29 days ago by
Michael Love26k
United States
Michael Love26k wrote:

You can use this code (just modifying so the -log10 pvalue is plotted instead of the LFC). Also you'd probably not want to bother adding the genes because there will be too many.

https://bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#plotting-fold-changes-in-genomic-space

~~For more details see the Gviz vignette.~~

This works if you've used tximeta to import the gene expression data. If you've used another pipeline, you'd need to manually add the locations if you haven't already done so.

ADD COMMENTlink modified 28 days ago • written 29 days ago by Michael Love26k

hello Michael thanks for answering my question, I looked at the 1st link you gave , it doesn't have a section on manhattan plots

ADD REPLYlink written 29 days ago by adeler0010

If you want specific help, can you provide more specific information about what you have?

How have you quantified gene expression? Are you using tximport/tximeta or some other counting tool?

Do you already have a DESeqDataSet with chromosome and start position for each gene, or do you need to know also how to obtain this information?

I have more specific recommendations after you've obtained the chromosome and start position:

You can use Sushi::plotManhattan as described here:

https://bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

Or you can use ggbio::plotGrandLinear as described here:

http://bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf

ADD REPLYlink written 28 days ago by Michael Love26k

Hello Michael . I did not use tximport/tximeta. I used featurecounts to get the read counts, I dont have the chromosome positions , how can i include that information ?

ADD REPLYlink written 28 days ago by adeler0010

Take a look at the Rsubread vignette. They have some information on extracting information about the annotation.

ADD REPLYlink written 28 days ago by Michael Love26k
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