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Using MapMan

How to use Ensembl identifiers in MapMan?

Hi All,

I am new to Mapman.

Is there any way we can feed the Ensembl identifiers or Uniprot identifiers to Mapman? Our annotation (Oryza Sativa Indica) have the ids from Ensembl genes (eg: BGIOSGA002746) & Uniprot identifiers (eg: Q9AWS9). It will be great if someone can suggest some converters for the purpose also.

All helps are appreciated.

Thank you.
Athul

RE: How to use Ensembl identifiers in MapMan?
Answer
10/25/18 12:53 PM as a reply to Athul Menon.
Hi

if you are ok with using the X4 annotation tree ( not all maps transferred yet).

Have a look here
https://github.com/usadellab/usadellab.github.io/tree/master/MapManJS/MappingFiles
this is ENSEMBL v39, we will likely skip v40 and use v41 again.


Otherwise you can always use Mercator X4 it should generate what you need within minutes (if you use proteins to annotate, transcripts is slower but should still be very quick)
http://www.plabipd.de/portal/web/guest/mercator4

Best Wishes
Björn

RE: How to use Ensembl identifiers in MapMan?
Answer
10/25/18 12:55 PM as a reply to Björn Usadel.
Ps In general one of the purposes of Mercator X4 is to make Id conversion obsolete as long as you have the protein FASTA use that one.

RE: How to use Ensembl identifiers in MapMan?
Answer
11/9/18 4:51 AM as a reply to Björn Usadel.
Björn Usadel:
Hi

if you are ok with using the X4 annotation tree ( not all maps transferred yet).

Have a look here
https://github.com/usadellab/usadellab.github.io/tree/master/MapManJS/MappingFiles
this is ENSEMBL v39, we will likely skip v40 and use v41 again.


Otherwise you can always use Mercator X4 it should generate what you need within minutes (if you use proteins to annotate, transcripts is slower but should still be very quick)
http://www.plabipd.de/portal/web/guest/mercator4

Best Wishes
Björn


Thank you for prompt reply. I will have a look into that.

Regards,
Athul