Question: RNAseq Rice: multiple condition testing and annotation
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gravatar for dina.hesham139
2.7 years ago by
Egypt
dina.hesham139120 wrote:

Hello,

I'm working on Rice rnaseq data. Kallisto was used for the pseudo-alignment. I have to questions:

1- I have 6 conditions 2 replicates each (12 samples in total), how can I do multiple condition testing to get the differential expressed genes? I tried sleuth and deseq2 but I couldn't do all the conditions at once. is there a way to do that?

2- The gene names are in that format : OS11T* , I can't do the further gene annotation for the genes? Any idea how to do it?

Thanks in advance.

rna-seq rice • 777 views
ADD COMMENTlink modified 2.7 years ago by h.mon31k • written 2.7 years ago by dina.hesham139120
0
gravatar for h.mon
2.7 years ago by
h.mon31k
Brazil
h.mon31k wrote:

Question 1)

Although I think it is rarely interesting, edgeR can do this, see "3.2.6 - An ANOVA-like test for any differences" at the edgeR Users Guide.

edit: see this discussion for a detailed discussion about what exactly is being tested.

Question 2)

Probably GrameneMart or BioMart can convert and / or further anotate your genes.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by h.mon31k

Thank you! I will give it a try!

ADD REPLYlink written 2.7 years ago by dina.hesham139120
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