Rattus norvegicus RGSC 6.0/rn6 genome database

[alussier17]

Hello,

I would like to use your software on sequencing data aligned to the newest R. norvegicus genome (RGSC 6.0/rn6). Could you please add it to your annotation database?

Cheers,

alussier17

[ny-shao]

Hi alussier17,

I'm sorry but unfortunately the current Ensembl is still old rn5 version.

ftp://ftp.ensembl.org/pub/release-78/gtf/rattus_norvegicus/

region_analysis need the biotype information from Ensembl, so now we can't add rn6. I will keep this thread open and when Ensembl update their database I promise I will add it.

Best,
Ning-Yi

[alussier17]

Hi Ning-Yi,

That's unfortunate... thank you for letting me know and for your quick reply. Hopefully, it will be up relatively soon.

Cheers,

alussier17

[VivekTodur]

Hi,

Now it is available. Could you please add Rno6. Or at least can you explain how to prepare the database...??

thanks,
Vivek

[subhoshreeghose24]

Hi,

I am also trying to perform region analysis with my DMR file (diff.nb.txt format) but getting an error of unsupported genome. So it would be really kind if you add this to the default browser. I tried with the refFlat rn6 file downloaded from ucsc but it is not supporting...

Thanks
Subhoshree

[VivekTodur]

Hi Subhoshree,

Once you download the refFlat, just need to reorganize the columns and the example for the same is here,

Vom2r1 NM_001099461 1 - 245887 267011 245887 267011 7 245887,256156,257489,258566,259804,260546,266805, 246774,256280,257714,259370,260077,260562,267011,

But the only thing I am not sure is the way to define the path for a newly created database, kindly share if you figured out this.

Thanks
Vivek

[subhoshreeghose24]

okay I will definitely try this...But the issue was initially that when I am running the command with( .txt) file and a ( -g) before that it is always showing unsupported genome.....

[VivekTodur]

Yeah, rn6 is basically not supported. So try with rn4 it should work fine. If it works fine then next challenge is to prepare the database and storing in the right path, where the tool is capable of reading it.

Vivek

[subhoshreeghose24]

okay...So you are suggesting I should run my diffReps output file (diff.nb.txt) which has been done with rn6 with rn4 region analysis and later on liftover the coordinates using ucsc.....I will try that then Subhoshree Ghose CSIR-SRF C/O Dr. Shantanu Sengupta Lab No. 201 CSIR-IGIB

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On Tue, Jan 16, 2018 at 12:25 PM, Vivek Todur ***@***.***> wrote: Yeah, rn6 is basically not supported. So try with rn4 it should work fine. If it works fine then next challenge is to prepare the database and storing in the right path, where the tool is capable of reading it. Vivek — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#29 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AhuznwLGPPezuZFVkjOIctjUV2d4BgRNks5tLEfIgaJpZM4DV9un> .