Question: How to feed Deseq in Galaxy with custom count tables?
gravatar for vebaev
2.7 years ago by
vebaev130 wrote:

Hi, In Galaxy it says Deseq is using count tables for each sample from htseq-count.
I want to feed Deseq with custom count tables (not generated from htseq-count) but it gives me error.

The tables are tab formatted as this, and each sample have same ids:
Contig_000039 159
Contig_000040 49
Contig_000041 4
Contig_000042 6
Contig_000043 2
Contig_000044 0
Contig_000045 2
Contig_000046 2

So probably I'm going something not as Deseq is especting :)

PS the error I got from Galaxy:
Warning message: In levels<-(*tmp*, value = if (nl == nL) as.character(labels) else paste0(labels, : duplicated levels in factors are deprecated Error in DESeqDataSet(se, design = design, ignoreRank) : design has a single variable, with all samples having the same value. use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used Calls: DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet

count tables deseq • 896 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by vebaev130
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is an input data format problem. If you want to use custom counts, then it must match the dataset format that htseq_count produces. See the tool form within Galaxy for details in the help section. You could also run it on a sample of your data to review exactly what the format is, then match it with your custom counts.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
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