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Analysis advice for RNAseq: WT/KO, treated & control, 3 time points.

Hello all, I've really hit my analytical limits with the current experimental design, I have RNAseq of cells from a KO model (and WT cells as well) that were treated over 3 different time points.

I use Orange 3 for my data mining, but I don't think the Bioinformatics window is very intuitive to use.

Do you have any suggestions of software, environements, packages that can accomodate such a kinetic experimental design in 2 different conditions?

Also I have done the sequencing through a core facility and the file I have on hand is a normalised expression matrix, I also have the non-normalised matrix.

I'll be happy to share the data if someone can guide me through the analyses.

Thanks!

rna-seq
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updated by Ram Ram • written by fazoup2 • fazoup2

heeeeeelp!

This is really bad etiquette. Please don't do this. I've removed this from your title.

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written by Ram Ram

I'm sorry, I am new to the community. I could delete the post and reformulate the question if you wish.

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written by fazoup2 • fazoup2

1 answer

Bioconductor has an excellent vignette that covers many aspects of RNA-seq analysis, including analyzing time series data in DESeq2. For this you will most likely be including an interaction term in your regression model during differential expression. More information on the DEseq2 library can be found in their vignette.

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written by rpolicastro rpolicastro

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