Hi all
I am working with soybean, and very excited to see that you have applied this system to tailor MapMan to the GeneChips
of two model legumes, Glycine max and Medicago truncatula.

I can't find the Mapping of Glycine max on the site http://www.gabipd.org/database/java-bin/MappingDownloader.

May I have a copy of maping file please?

Thank you very much !

Anny

email: anny424 atti gmail.com

Dear Anny,

we can create a glycine max mapping (as there is none yet) using our automated annotation pipeline. To do so we would need sequence information. If you are interested in using the Affymetrix soybean chip i can use the soy targets sequences available from their webpage to create the mapping. If you would like to have a mapping for another set of soybean sequences, please let me know which one you'd prefer.

best greetings,
Marc

Dear Dr Marc Lohse

My name is Takeshi Furuhashi. I am postdoc at Metabolic Systems Research Team in Riken Institute, Japan.

I am looking for mapping file of soybean (Glycine max). As I have used custom made array, I had trouble for using Mapman.
Is there any possibility that you can develop Mapman mapping file for us? This can be very helpful for people who are using same microarray.

GPL13674 is platform name.
You can know about gene number.

Alternatively, can you introduce other informatics people for asking such issue?

Sorry for interrupting your precious time.
Sincerely, Takeshi

Hello I am trying to upload soybean mapping file Gmax_189. when i am uploading file it shows error:
Error during data configuration, at least one data column should be selected. kindly help me to upload mapping file.Thanks

Hi,

I am not entirely clear which step you are having difficult with.

If you need to load the mapping file for Gmax_189 into mapman, then these are the steps you need to follow in the MapMan application:-

- Right click on 'Mappings' -> New Mapping -> download
- Select 'Glycine max/Gmax_189: 1.0' from the list

This should load the mapping file into the MapMan application.

Regards,
Marie.

Dear Marie
Thank you so much for guiding me.I finally succeeded in uploading file. Mapman forum is very useful for new learners.

Dear Marc,

Thank you for your interesting in creating a glycine max mapping.
We are very interested in using the Affymetrix soybean chip.

The raw sequence data from the genome sequencing projects is on the site: http://www.phytozome.net/soybean

The SoyBase Affymetrix ™ GeneChip ® Soybean Genome Array Annotation is on the site: http://soybase.org/AffyChip/index.php.
In this annotation, the Affymetrix Probe set ID has mapped to the genome sequencing ID, AGI, and GO annotation. Maybe they are helpful.

Hope for your excellent work!
All the best!

best greetings,
anny

Dear Anny,

i am working on mappings for both platforms now - as soon as both of them are finished i'll let you know via this forum.

bests,
Marc

Hi Anny,

the mapping for the Affymatrix platform is ready and available for download from within mapman. If you need the clear text format file please send my a reply adress and i'll be happy to send it to you.

Bests,
Marc

Marc,

I saw this post. Could you email me a clear file text format file for Clycine max? How do you annotate each Affy probeset?

Many thanks

Charles

Hi Charles,

the soy bean mapping is also available in the MapManStore, our public repository for mapping
files. You can download it directly from there: http://mapman.gabipd.org/web/guest/mapmanstore

Best greetings,
Marc

Dear Marc,

Thank you very much for your help.
I used the mapping to analyze my data, it's vey useful and convenience.
Moreover, I would like to get the clear text format file of it.
My email: anny424@gmail.com

best greetings,
anny