Reapload a usable Readcount file?

Question: Reapload a usable Readcount file?

21 months ago by

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

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modified 21 months ago by Devon Ryan • 1.9k • written 21 months ago by lena_fuchs3 • 0

21 months ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k 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 COMMENT • link written 21 months ago by Devon Ryan • 1.9k

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 REPLY • link modified 21 months ago • written 21 months ago by lena_fuchs3 • 0

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 REPLY • link written 21 months ago by Devon Ryan • 1.9k

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