Question: Read alignment plot for RNA-Seq data
0
gravatar for mike
3.3 years ago by
mike60
Germany
mike60 wrote:

I am having RNA-Seq data with 5 replicates per condition. I want to look at the coverage (read alignment) for a particular genes for these condition. Whats the best possible way to take average of 5 replicates per condition and check the coverage? I have already checked it for a single replicate with Gviz package in R.

Thanks

rna-seq • 1.1k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by mike60
2

You can make a box plot or just plot the points across all conditions for each replicate. DESeq2 has an option called plotCounts which does the same.

I use a wrapper around plotCounts to plot the boxplot ( as I have more than 20 samples per condition ) for multiple genes,

plotGeneCounts <- function (dds, genes, intgroup) {
  for (i in 1:length(genes)) { 
    x <- plotCounts(dds, gene=genes[i], intgroup=intgroup, transform=TRUE, returnData=TRUE)
    x$gene=genes[i]
    if (exists("gene_vec")){
      gene_vec <- rbind(gene_vec,x)
    } else {
      gene_vec <- x
    }
  }
  ggplot(gene_vec, aes(x=factor(intgroup), y=count))+geom_boxplot(aes(fill=gene))+facet_wrap(~gene, scales="free")
}

Use:

genes <- c("INS","IAPP","PDX1")
plotGeneCounts(dds,genes,"treat")

Where dds is a DESeq2 object.

EDIT: I understand that you would like to show the coverage across the gene structure. For this, you could simply create the track hub for ucsc browser for all your samples and show the coverage as overlay mode, separately for treated and untreated.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by geek_y10k

Thanks but I am looking for this image. I was able to generate this with Gviz but only with 1 replicate per condition. How can I take read counts for all replicates per condition and generate the same plot?

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by mike60
0
gravatar for mike
3.3 years ago by
mike60
Germany
mike60 wrote:

Thanks but I am looking for this image. I was able to generate this with Gviz but only with 1 replicate per condition. How can I take read counts for all replicates per condition and generate the same plot

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by mike60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 976 users visited in the last hour