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mapping maize file not working... transcript ID vs gene ID problem ??

Hi All,


I just tried to run my own maize RNAseq data in Mapman and it seems that something is not working properly: I got pathways with circles instead of squares, and they have no values (all circles are grey, and don't have any identifier when I put the mouse on them).
Anyone knows what could be going on? I would much appreciate any help :-)

I have no idea what the problem could be, but one of my hypothesis is that maybe it could be related with the fact that I am using the Zm_B73_5b_FGS_cds_2012 mapping file, that as has transcript identifiers while my own data have gene identifiers. I removed all the _T01, etc. from the file, but I think there is still a problem because now the mapping file has redundancy lines (several lines with the same gene ID). Anyone has been through thas kind of problme before? It would be veeery time consuming to manually remove all the redundancy line from the mapping file, and I was wondering if there could be any other solution....

Thanks in advance for your help!


Best,


Paula

RE: mapping maize file not working... transcript ID vs gene ID problem ??
Answer
3/16/17 1:52 AM as a reply to paula doblas.
Hi,

I came cross the same situation. Do you make it?

RE: mapping maize file not working... transcript ID vs gene ID problem ??
Answer
3/16/17 7:31 AM as a reply to HAILONG YANG.
Hi
did you use one of the supplied pathways?

If you get circles instead of squares this is an indication that MapMan tries to visualizued metabolitte data. Try rightclicking on a stack of glyphs and try changing the "type" there.

Best
björn