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Question: CRISPRseek: create own org.Hs.eg.db package
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gravatar for Julie Zhu
2.4 years ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:

Yacine,

 

Sorry that I misread your message.  Marc Carlson is the developer of the annotation package org.Hs.eg.db. http://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html. If you post the message, Marc should be able to see it. Here is a post about creating your own org.Xx.eg.db package. problem creating own org.Ss.eg.db

FYI, you can leave this parameter out when you run offtargetAnalysis. This package is for assigning gene symbol to the off target sites.

Best regards,

Julie

 

From: Yacine Badis <Yacine.Badis@sams.ac.uk>
Date: Thursday, June 25, 2015 12:11 PM
To: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Subject: RE: Create gene ID mapping package .db for use in CRISPRseek

 

Many thanks for your answer Julie,

 

Unfortunately (for me J ) my question was strictly related to the org.Hs.eg.db file mentioned in your pdf, but maybe Herve would have more infos on this. I have no problem with BSgenome and TxDb objects, I got help already from bioconductor support website for this. I would post this but the site has been blocked since yesterday on my laptop, I will post it soon, but still seek for an answer.

 

Many thanks in advance,

 

Yacine

 

From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu
Sent: 25 June 2015 16:15
To: Yacine Badis
Subject: Re: Create gene ID mapping package .db for use in CRISPRseek

 

Dear  Yacine,

 

Thanks for the feedback! Could you please post your message at https://support.bioconductor.org so that others can contribute and benefit? Many thanks!

 

Here is how to forget your own bsgenome at http://www.bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf . If you post this at the support site, Herv´e Pag`es the developer of BSgenomeForge will be able to see your question as well.

 

http://www.bioconductor.org/packages/release/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf has the information on how to make your own txdb object. 

Best regards,

Julie

From: Yacine Badis <Yacine.Badis@sams.ac.uk>
Date: Thursday, June 25, 2015 5:28 AM
To: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Subject: Create gene ID mapping package .db for use in CRISPRseek

 

Dear Julie,

 

First of all, thanks for your release of CRISPRseek, I am very interested by this package, as I try to develop my (rather poor) bioinformatics skills. I have been creating TxDb and BSgenome objects for my Model organism to use your package. My final step would be to create a . db file as the one required in your examples org.Hs.eg.db. But I cannot find a way/tool to create this. As I could not find the information elsewhere, could you please tell me if such a tool exist?  I have a genome (assembled in supercontigs, not chromosomes ), a gff3 file, and RNAseq datasets. I also had a basic question about the min/max number of RE sites to search for, and possibly a way to find this NEBenzymes.fa file?

 

Many thanks in advance for your answers,

 

Yacine Badis

++++++++++++++++++++                                                                                                                                                                                                                               Dr Yacine BADIS                                                                                                                                                                                                                                 Postdoctoral Researcher and Teaching Associates                                                                                                                                                                                   Scottish Association for Marine Science

Scottish Marine Institute
PA37 1QA Oban
United Kingdom
Yacine.Badis@sams.ac.uk
Tel: 0044 16 31 559485
++++++++++++++++++++

ADD COMMENTlink written 2.4 years ago by Julie Zhu3.8k
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