Question: Reapload a usable Readcount file?
gravatar for lena_fuchs3
21 months ago by
lena_fuchs30 wrote:

Hi All,

I have a question, I try to compare two different runs of RNA sequencing. However the different runs seem to have different Baselines in Readcounts one pretty always double the other. So I downloaded the tabular file and divided the samples from the first run by 2. Afterwards I wanted to upload it again and run differential count models (edge R/ voom/...). The uploaded file looks just like the old one when I view it in galaxy,however the outcome files are empty when I try to do the differential counts again. Does anyone know if its possible to download and reupload a readcount file, being usable? And if yes how? stderr: Error in read.table(Input, header = T, row.names = 1, sep = "\t") : duplicate 'row.names' are not allowed Cheers and thank you, Lena

rna-seq galaxy • 490 views
ADD COMMENTlink modified 21 months ago by Devon Ryan1.9k • written 21 months ago by lena_fuchs30
gravatar for Devon Ryan
21 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

There is no reason to divide the counts in half, edgeR/voom and similar tools will handle that automatically.

The actual error you're seeing is due to a duplicated gene name. If you didn't see this with the original files then you must have accidentally changed the first column before you uploaded.

ADD COMMENTlink written 21 months ago by Devon Ryan1.9k

Hi Devon, thanks for answering. Are you sure it'll be handled automatically? I have the read counts of both runs in one file- I had two samples of a treatment group and 2 of a control group in run 1, two of each in a second run later. The counts in one run seem to be in general about double to the other. I can't imagine how it could get that half of the sample in each group are different: Meaning if expression would double, the counts could be 8,8,16 and 16 in the control group and 16;16, 32 and 32 in the other-won't that make it much harder to gain significance? I did not change the first column, I tried again to make sure. I feel it is because I have to open it with excel, but I couldn't figure out how else I could open it. Sorry I am a newbie, would be great if you could send a text back Thanks Lena

ADD REPLYlink modified 21 months ago • written 21 months ago by lena_fuchs30

I can guarantee that all even remotely modern RNAseq tools handle this properly. A 2x difference in depth is generally not a problem, though you start running into issues once the difference is around 10x.

ADD REPLYlink written 21 months ago by Devon Ryan1.9k
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