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RNA seq Arabidopsis thaliana

RNA seq Arabidopsis thaliana
rna seq
Answer
1/25/13 11:12 AM
Hi!

I have data from a RNA seq in Arabidopsis thaliana. I have a list of genes that change their expression comparing results between a mutant and a control. I tried to visualize the data using mapman, however I had problems because mapman didn't recognize my gene agi numbers (an example of this number: AT3G14415.2). It seems that mapman only recognize numbers from microarrays (an example of this number: 244901_at). I suppose that I didn't download the proper version of mapman or that I didn't set the right options for my purpose. Could anybody give me some instructions to solve this problem?

Thank you!

Daniel

RE: RNA seq Arabidopsis thaliana
Answer
1/25/13 11:23 AM as a reply to Daniel Caudepon.
Hi Daniel,

MapMan can perfectly visualize your data - the problem is that you have accidentally chosen
the mapping file for the ATH1 array. Please choose the mapping called Ath_AGI_ISOFORM_MODEL_TAIR10_Aug2012
from the list of mappings in the tree view on the left half of the MapMan main window. If this mapping
file is not listed there, you can download it directly fron within MapMan by right-clicking on "mappings"
in the tree view and then choosing "new mapping"->"download". A dialog box listing all available mappings
will pop up and you can select the mappings you would like to obtain.

I hope this solves your problem.

BTW: When working with RNA-Seq data you might find RobiNA (another tool we develop) quite
useful for quality checking, filtering and statistically assessing differential gene expression.

Visit: http://mapman.gabipd.org/web/guest/robin

cheers,
Marc

RE: RNA seq Arabidopsis thaliana
Answer
1/25/13 5:08 PM as a reply to Marc Lohse.
Thank you very much!
Best wishes,
Dani.