Question: RNA-Seq differential gene expression without biological and technical replicates.
0
gravatar for utsafar
9 weeks ago by
utsafar40
utsafar40 wrote:

What I have is six RNA-Seq datasets from three developmental stages in two conditions (control and treatment), without biological and technical replicates. (I did all the following in usegalaxy.eu) Each dataset was mapped to reference genes using tophat. htseq-count was used to count aligned reads. I tried to use DESeq2 for differential expression analysis but it works only when I have replicates. Is there any way/tool to do DE without biological and technical replicates? suggestions considering Galaxy friendly tools are preferred. Thank you so much

Note: The data belongs to a friend who said that they have no replicates because of budget shortages.

rna-seq • 242 views
ADD COMMENTlink modified 6 weeks ago by a4106387580 • written 9 weeks ago by utsafar40
1

If you wish to get galaxy specific advice you may want to post this over in Galaxy help forum: https://help.galaxyproject.org/

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax89k
2
gravatar for sambhav2mishra
9 weeks ago by
sambhav2mishra20 wrote:

You can try using edgeR package (go through edgeR manual) , it has an explanation where you can analyse DGE without any replicates. Thanks

ADD COMMENTlink written 9 weeks ago by sambhav2mishra20
1
gravatar for Ido Tamir
9 weeks ago by
Ido Tamir5.1k
Austria
Ido Tamir5.1k wrote:

How to run the Deseq2 tool without replicates. maybe look at NOI-Seq http://seqanswers.com/forums/showpost.php?p=107433&postcount=2

or just do it in excel: sort by ratio from high to low, same reliability (but no normalisation). The result is not to be trusted. It would have been better to use just 1 developmental stage or only control or treatment in a time course. Then the data would have been at least somehow reliable. RNA-Seq data is noisy and you simply don't know which of the > 20000 data points represents a reliablel difference without replicates.

ADD COMMENTlink written 9 weeks ago by Ido Tamir5.1k
0
gravatar for eyonesi
9 weeks ago by
eyonesi40
eyonesi40 wrote:

Deseq, edgR and bayseq are pakages that can analyze without replicate. But, i think, they require replicate when running in the galaxy. Regardless of the galexy, edgR and Bayseq can be better choices for anlyses without replicat.

ADD COMMENTlink written 9 weeks ago by eyonesi40
0
gravatar for a410638758
6 weeks ago by
a4106387580
a4106387580 wrote:

You can use NOIseq or edgeR to process samples without biological and technical replicates

ADD COMMENTlink written 6 weeks ago by a4106387580
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