I was trying to visualize the Brachy RNA seq data after i got answers from you guys and I am getting the error message that mappings is not identical. When i clicked the detail icon to see the details of error, I found my gene ids (e.g bradi2g19640.1). is not matched with mappings, which has bradi2g19640.1|pacid:21803018.
Is that the normal problem? or can you suggest the way to find the pacids for the gene ids or somehow ignore that so that my genes ids can match with mappings. I have gene ids from phytozome though.
Hope i made my point clear.
Thanks in advance for the help.

Prateek

Hi Prateek,

the mapping you used was derived from the sequences available from Phytozome v9.0 - when generating
this mapping, we used the IDs as supplied with the sequence data sets. This is was causes your problem -
that is relatively easy to solve, though: Just obtain a txt or Excel version of the mapping file and remove all the
"|pacid:21803018"-like segments from the ID column and save the result using a different name. Now you can use
your modified mapping file in MapMan to visualize your data.

I hope this helps,
bests,
Marc

Hello Marc,
Thanks for reply. I hope it should solve the issue. However, what will be the easiest route to get the .txt file of mapping?

Prateek

I got the .txt file form store.
Thanks. Will try and will be back, if that doesn't work.

Thanks again.

Prateek