DEXSEQ error (no counts falling in this gene, there is nothing to plot).
1
0
Entering edit mode
@huckthornton-23681
Last seen 13 months ago

Hi all,

I have been trying to use the plotDEXSeq function and received the following error: "No read counts falling in this gene, there is nothing to plot."

I want to understand what this means and ask if there is anyway to fix this problem.

Best wishes,

XXX

plotDEXSeq(dxr, "gene", legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )

software error • 148 views
ADD COMMENT
0
Entering edit mode
@kevin
Last seen 52 minutes ago
Republic of Ireland

Hi, the error can be interpreted as literally as is stated:

No read counts falling in this gene, there is nothing to plot

If you feel that there should be counts for this gene, then, perhaps, check the reads overlapping the gene's exonic co-ordinates in your BAM files (using, e.g., samtools) - they may have been flagged. You could also load the BAM's alignments into IGV and view them in that way (if they exist).

If you find that reads do indeed overlap the gene's exons, then please paste all of your commands across all programs so that any of us could begin to properly diagnose the issue.

Kevin

ADD COMMENT
0
Entering edit mode

I think it should overlap the gene's exons.

library(DEXSeq)
countFiles = list.files("/user/XXX/fasta", pattern = "gene.counts.txt$", full.names = TRUE)
basename(countFiles)
flattenedFile = "/user/XXX/annotations_gene_hg38.gff"
sampleTable=data.frame(row.names=c("A", "B", "C", "D", "E", "F"), condition=c("U","U", "U", "D", "D", "D"))
head(sampleTable)
dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design=~sample + exon + condition:exon, flattenedfile=flattenedFile)
dim(dxd)
dxd=estimateSizeFactors(dxd)
test<-counts(dxd, normalized=T)
write.table(test, file="/user/XXX/fasta/normalized_counts_DEXSeq.txt", sep="\t",  row.names = TRUE, col.names = TRUE)
dxd=estimateDispersions(dxd, BPPARAM=MulticoreParam(workers=16))
dxd=testForDEU(dxd, BPPARAM=MulticoreParam(workers=16))
dxd=estimateExonFoldChanges(dxd, fitExpToVar="condition", BPPARAM=MulticoreParam(workers=16))
drx=DEXSeqResults(dxd)
write.table(drx, file="/user/XXX/fasta/test_DEU_all.txt", sep="\t", quote=F, row.names = TRUE, col.names = TRUE)
plotDEXSeq(drx, "gene", legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2)
ADD REPLY
0
Entering edit mode

I think it should overlap the gene's exons.

Can you provide evidence for this, please?

ADD REPLY
0
Entering edit mode

For example, try my suggestions regarding IGV and samtools.

ADD REPLY

Login before adding your answer.

Traffic: 284 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6