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Using MapMan

General query for RNA seq data

General query for RNA seq data
Answer
8/1/13 2:26 AM
I was wondering to know how much data will be covered by the Mapman for a RNA seq data for Brachypodium. I mean definitely, their must be some number of genes which are nit going to map to given bins in the mappings.

RE: General query for RNA seq data
Answer
8/1/13 11:17 AM as a reply to Prateek Tripathi.
Hi
just a general answer. If you ran your trascriptome through Mercator or it is based on the newest one, all genes will be mapped.
That said this includes the "we really don't know what it does bin" 35.
In general you can expect that about 50% of the protein coding genes will be in there. (This sounds worse than it is, even for Arabidopsis there really is no good classification for more than 1/3 of all the genes =>35)
Now in addition come -of course- all the other goodies you might find: Novel genes in your data set and if you sequence small RNAs these will mostly not be mapped.

I hope this helps in genral.

Cheers
björn

RE: General query for RNA seq data
Answer
8/1/13 11:26 AM as a reply to Prateek Tripathi.
Hi Prateek,

this also depends on what Brachypodium reference transcriptome you mapped your RNA-Seq data against. We
provide a MapMan mapping based on the sequences available from Phytozome (release 9.0). If you mapped
your RNA-Seq reads against this data set, you can obtain the mapping from our repository (http://mapman.gabipd.org/web/guest/mapmanstore)
and visualize the data in MapMan. If you built your own transcriptome assembly based on the reads you could
generate a MapMan mapping using the mercator tool (http://mapman.gabipd.org/web/guest/app/mercator) and
then use this custom mapping to work with your data (as pointed out by Björn).

I hope this answers your question?

cheers,
Marc