Can I use Mapman to view pathways for maize RNA-sequencing data obtained from next generation sequencing?

Thomas

Dear Thomas,

In principle RNAseq data is no problem, you would just have to express it on a log scale relative to something.
Let's say you have treatment and control
then you would prepare a table with
GeneId TvsC
111 log2(FPKM gene 111 treatment/FPKM gene 111 control)
112 log2(FPKM gene 112 treatment/FPKM gene 112 control)

and so forth.

You could also just logs your data for e.g. time course data, but as the coloring changes from one color to the other at zero it is probably a good idea to reference it to something.

However, if this is an issue that is coming up (e.g. in time courses) we could e.g. provide a rainbow scale or think together about an optimal solution

Cheers,
Björn

Thanks Bjorn. The data is organized as log 2(treatment/control). The gene ID is annotated according to Maize Genome Database (e.AC147602.5_FGT002, GRMZM2G315349_T01) from http://www.maizegdb.org/
The current maize mapping files is for affymetrix chips so I won't be able to use them. I have only the gene/transcript ID but not the sequence. will I still be able to use Mecator to create a new mapping files?

thomas