Question

DEXSEQ error (no counts falling in this gene, there is nothing to plot).

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huck.thornton ▴ 10

@huckthornton-23681

Last seen 4.4 years 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 • 899 views

ADD COMMENT • link updated 4.5 years ago by Kevin Blighe ★ 4.0k • written 4.5 years ago by huck.thornton ▴ 10

Kevin Blighe · Answer 1 · 2020-06-15

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Kevin Blighe ★ 4.0k

@kevin

Last seen 6 weeks 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 • link 4.5 years ago Kevin Blighe ★ 4.0k

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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 • link updated 4.5 years ago by Kevin Blighe ★ 4.0k • written 4.5 years ago by huck.thornton ▴ 10

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I think it should overlap the gene's exons.

Can you provide evidence for this, please?

ADD REPLY • link 4.5 years ago Kevin Blighe ★ 4.0k

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For example, try my suggestions regarding IGV and samtools.

ADD REPLY • link 4.5 years ago Kevin Blighe ★ 4.0k