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citrus mapping

Szálak [ Előző | Következő ]
citrus mapping
Válasz
2019.11.14. 7:58
Hello,
I`m working with Citrus Sinensis sequence, reference type: locus ID (PLAZA3.0). Is there any way to upload it to the mapping file for using as a reference.
thanks,

RE: citrus mapping
Válasz
2019.11.14. 10:37 válaszként erre: siwar I. assili.
Hello Siwar,

We actively maintain the mapping files for only a select number of species on our download site (mainly the EnsemblPlants genomes)

However, you can easily submit the Citrus Sinensis sequences to Mercator4 yourself and the output you obtain is the 'mapping file'.

https://www.plabipd.de/portal/mercator4

If you have any problems submitting or retrieving the mapping file, please let me know.

Regards,
Marie.

RE: citrus mapping
Válasz
2019.11.19. 13:50 válaszként erre: Marie Bolger.
Hi Marie,
I converted my data to Citrus Sinensis phytozome: Csinensis_154, and I downloaded the mapping file from your web. as required, but I still can't run it on MapMan.
examples of genes ID from my work:
orange1.1g013346m
orange1.1g005037m
orange1.1g012820m
orange1.1g040288m
orange1.1g042954m
orange1.1g025077m
orange1.1g009399m
orange1.1g043627m
orange1.1g029568m
orange1.1g027229m
orange1.1g005321m
orange1.1g046764m
orange1.1g003680m

RE: citrus mapping
Válasz
2019.11.22. 15:05 válaszként erre: siwar I. assili.
Hi Siwar,

I think there was a misunderstanding.

We do have a mapping file for Citrus sinensis in our store from which is from phytozome, but it is V1.0. (This can also only be used with the older pathway diagrams).

The only version I can see that is currently available on phytozome is V1.1 (which is the Csinensis_154 which your have used).
The gene id's have changed between these two versions.

However, you can download the Csinensis_154_v1.1.protein.fa.gz from phytozome and submit it to the new Mercator4 at
https://plabipd.de/portal/mercator4

The output of this can be used in MapMan together with you data and the pathway files (which start with X4.2_)

If you have any problems/questions, let me know.
Regards,
Marie.