mm10 for running CEAS locally!

[doanduy...@gmail.com]

Dear Jian,

because the mouse genome mm10 is still not available in Cistrome plattform, I've installed CEAS locally and tried to download pre-compiled gene annotation tables for mm10. However I realized mm10 sqlite3 file is also not available on http://liulab.dfci.harvard.edu/CEAS/download.html. It will be a great help if you could tell me where I could get mm10 sqlite3 file? Thank you very much for your supports!

Doan Duy Hai

[Jian Ma]

Hi Doan,

If you have already downloaded the ceas package, there's a script called "build_genomeBG". You can use this to create the sqlite3 file. The command line for create mm10 is like this.

$ build_genomeBG  -d mm10 -g refGene -w <control_wiggle_file.wig> -o mm10.sq3

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best，

Jian Ma,

[doanduy...@gmail.com]

Thanks Jian!

Doan Duy Hai

[Calvin Tsang]

Dear Jian,

I came across your post. I am also trying to download the mm10.refGene sqlite3 file to my Linux computer.  I appreciate if you would tell me what is that -w <control_wiggle_file.wig> in the command you mentioned, and how can I download it? Sorry I am a new user of Linux and do not know much about the command. Thank you very much!

Calvin

   

On Thursday, June 4, 2015 at 9:19:46 AM UTC+8, Jian Ma wrote:

Hi Doan,

If you have already downloaded the ceas package, there's a script called "build_genomeBG". You can use this to create the sqlite3 file. The command line for create mm10 is like this.

$ build_genomeBG  -d mm10 -g refGene -w <control_wiggle_file.wig> -o mm10.sq3

2015-06-04 3:18 GMT+08:00 <doanduy...@gmail.com>:

Dear Jian,

because the mouse genome mm10 is still not available in Cistrome plattform, I've installed CEAS locally and tried to download pre-compiled gene annotation tables for mm10. However I realized mm10 sqlite3 file is also not available on http://liulab.dfci.harvard.edu/CEAS/download.html. It will be a great help if you could tell me where I could get mm10 sqlite3 file? Thank you very much for your supports!

Doan Duy Hai

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To unsubscribe from this group and stop receiving emails from it, send an email to cist...@googlegroups.com.

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best，

Jian Ma,