Mus musculus support

[mcc-]

Mus musculus is a commonly used model organism, and it would be useful to offer support for mouse data as well as human.

[ScaonE]

Any changes regarding Mus musculus support ?

Best regards

[dgautheret]

Within 2-4 weeks, we should have a new version of DEkupl-run and DEkupl-annotate supporting any genome...

[ScaonE]

I am eager to try it !
Thanks for your quick answer.

[khandarius]

Hi,

Are you releasing the Mus musculus -supported version any time soon? If not, could you describe the required changes in the code that would allow using your software with mouse data? I am very interested in using DE-kupl on my own mouse data.

Thanks,
Darius

[jaudoux]

Hi @khandarius, @ScaonE, @mcc-,

You can now use DE-kupl with Mus-Musculus genome (or any other genome).

DEkupl-run

When using DE-kupl run you will need to specify some parameters in the config file regarding the genome you are using :

• transcript_fasta the fasta transcriptome that you want to use. For example using Ensembl
• transcript_to_gene a file with the mapping of transcripts IDs to gene IDs. Such a file can be gerated with Biomart

DE-kupl annotation

For DE-kupl annotation, we have developed a new version that is still il beta but yet usable : https://github.com/Transipedia/dekupl-annotation/tree/new-version

In this version you have a dkpl index command that you will use to provide dekupl-annotation module with your genome and annotation files.

Do not hesitate to get back to me if you have difficulties using DE-kupl with Mus musculus.

Best,
Jérôme.