RNAseq Rice: multiple condition testing and annotation

Question

[dina.hesham139]

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.

Answer 1

[h.mon]

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.

[dina.hesham139]

Thank you! I will give it a try!