Dear MapMan users,
I am working with Medicago RNAseq data.
We work with an intermediate updated version of the Medicago genome.

1/ The mapping file Mt_Mt3.5_0411 for medicago genome is not optimal in our case because we do not have correspondance for all Mt ID.
2/ It is hard to create an updated mapping file for our Medicago data (i don't know if it is possible and how long this will take)?
3/ Do you know if it is possible to work with the Arabidopsis mapping file (probablly Ath_AGI_TAIR9_Jan2010 download) because we got associacion with the TAIR 10ID on your Medicago RNAseq data?
4/ Witch is the last updated Arabido mapman mapping file i need to use ideally then (TAIR 10)
5/ Sorry for my very naive last question: Is it possible to have more information on How a MapMan mapping files for Medicago is construct? it is just assigning new Medicago to their ortologs in the current A.thaliana BINs.

Thanks a lot for your help
Céline

Dear Celine,

using Medicago RNA Seq data should not be a problem as long as you've mapped your reads against the
gene identifiers used in the Mt 3.5 release. There is a mapping available for these IDs and all you'd have to
do is load your (tabular) log2 ratios of expression into MapMan and use the Mt_Mt3.5_0411.m02 mapping
(available from the MapManStore: http://mapman.gabipd.org/web/guest/mapmanstore or directly from within
the MapMan application by clicking "mappings"->"new mapping"->"download")

Best greetings,
Marc

I am a total beginner here and still a little confused by " mapped your reads against the gene identifiers used in the Mt 3.5 release." How can I do that? And mine is vitis, and I have RNA seq data.

Thanks so much!

Hi nefeli x xu,

sorry if my earlier response was not very clear. By the sentence you quoted i mean that the RNA-Seq reads have to
be aligned (mapped) to a certain reference sequence. After this alignment step, a counts table summarizing how many
reads mapped to each gene (or transcript isoform) has to be extracted and serves as the basis for assessment of
differential gene expression.

So, you are actually not mapping the reads against gene identifiers but against the actual
genes (sequences). If you are new to RNA-Seq based analysis of differential gene expression, you can try our RobiNA
tool (http://mapman.gabipd.org/web/guest/robin) which provides all steps of RNA-Seq based analysis of differential
gene expression in a user friendly graphical application.

I hope that answers your question - bests,
Marc