Hello,

perhaps my question has already been answered in the post ("Maize Affy ID vs gene ID") but I can't access that one (it says "You do not have the required permissions" although I can open other posts), if so, sorry...

I was wondering if the new (?) files from Zea mays genome release could somehow be transformed from transcript ID (GRMZM0089833_T01) to gene ID (GRMZM00089833). That would be tremendously helpfu!

I know that this way the specific-transcript-information gets lost but I feel that would be only a minor issue.

I also tried the Phytozome Maize (the .xls file was 0 KB ), but it also uses the transcript IDs.

Since I don't know how to make a ".m02" file, I can't delete the transcript-ID tags myself, any help or advice would be appreciated!

Best
Steffi

Hi Steffi

and thanks for your feed back. You can obtain the .txt table versions of all the mapping files
via the MapManStore and then either open them in Excel (via Text import) or use a Text
editor of your choice to open and modify the files. That said, simply deleting all the "_T01" etc.
identifier extensions will not create a functional mapping file because it will introduce a lot
of redundancy (which will make MapMan issue errors upon import). The redundant lines
would have to be eliminated prior to import into MapMan.

best greetings,
Marc

Hi Marc,

thanks for your reply!

Yes, I saw all of it in the MapMan store, just wanted to point out that this specific .xls didn't work - no big issue, since as you mentioned, the .txt file can be imported into Excel.

I hadn't considered the redundancies, thanks for pointing that out! I'll give it a try and try to remove duplicates without loosing Bins attached to only special ones...


How can I import a .txt file into MapMan as a mapping?


(I found another post "Modifying mapping files" that points to the MapMan User Manual section 3.1. and I would love to follow that but can't find the MapMan Manual at all! On the Website, under >Resources >Manuals, Tutorials.... there is no manual at all, unfortunately. And google searches also didn't find it...)


Thanks ahead,
best,

Steffi

Hi again,

the MapMan manual is actually distributed together with the software and
can be accessed from within MapMan by clicking the help button (the
one with the "i").

There, you will find the section that the post referred to ;-).

best greetings,
Marc

THANKS!

I was blind - was looking for a "help" labelling in the upmost menu and overlooked the big "i" button! Awesome!