How to using this tools when clone in located

[tiramisutes]

Hi, I want to use this tool to design sgRNA for my study plant genome, but I don't know how to use it when git clone in my Linux. So, can you give me a simple tutorial? Thanks.

[RoyRabinowitz]

Hi, Thank you for your interest in BE-FF. I'll be happy to assist you through our tool. First, did you try our webserver? It is the simplest way to use BE-FF http://danioffenlab.pythonanywhere.com/BE-FF Unfortunately, BE-FF is unable to automatically fetch genomes of plants. Therefore, if you with to target a single site, you may manually enter the DNA sequences [image: image.png] Otherwise, if you wish to analyze multiple sites, you may use the batch mode: http://danioffenlab.pythonanywhere.com/upload You just need to download the template file and put in your sequences. Then, upload it to the same page and the results file will be automatically downloaded to your computer.

I hope this helps you. If you need any help with the code on git, please do not hesitate to contact me for further assistance.

Best, Roy

On Wed, Jul 1, 2020 at 3:38 AM hope notifications@github.com wrote:

Hi, I want to use this tool to design sgRNA for my study plant genome, but I don't know how to use it when git clone in my Linux. So, can you give me a simple tutorial? Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/RoyRabinowitz/BE-FF/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANEH4AYUASQX5FQ35AFW3TTRZKAOXANCNFSM4OM4VB6A .

--

Roy Rabinowitz, PhD Student Prof. Daniel Offen's Neuroscience lab Felsenstein Medical Research Center Sackler School of Medicine Tel-Aviv University

[tiramisutes]

Thanks for your reply. Yes, I have tried the webserver (http://danioffenlab.pythonanywhere.com/BE-FF) and want to use the second method for my study genome. But no species include in this webserver. So, I clone this code and want to supply the genome fasta file in my Linux. Now, I have genome fasta and annotation (gff3/gtf) files for my study species. But how to use it? By the way, through Google I know this code is writes using the Flask web framework. So, I run is with python Web/app.py after clone it. But there is a stderr with no found of BE-FF.html and give me a empty pages when open with firefox.

[RoyRabinowitz]

Basically, for each query (SNV) you need the following parameters to run the code:

1. the reference nucleotide
2. the variant nucleotide
3. upstream sequence
4. downstream sequence
5. reading frame value (1/2/3) - optional but very recommended (see the help page for more details http://danioffenlab.pythonanywhere.com/help )

Once you have these parameters, you may use the webserver or the code. If you want to use the webserver, create a csv file with your data (according to the template file). For using the script, download the following files from the git: BEMain.py , baseEditorsTable.py https://github.com/RoyRabinowitz/BE-FF/blob/master/Scripts/baseEditorsTable.py , BEseqType.py https://github.com/RoyRabinowitz/BE-FF/blob/master/Scripts/BEseqType.py (this is the parsing file), transverse.py https://github.com/RoyRabinowitz/BE-FF/blob/master/Scripts/transverse.py If you wish to use other fetch and parsing approaches, look for BEseqType on the main file and fetch the sequences as you'd like.

Please let me know if you have any questions

Roy

On Thu, Jul 2, 2020 at 12:13 PM hope notifications@github.com wrote:

Thanks for your reply. Yes, I have tried the webserver ( http://danioffenlab.pythonanywhere.com/BE-FF) and want to use the second method for my study genome. But no species include in this webserver. So, I clone this code and want to supply the genome fasta file in my Linux. [image: image] https://user-images.githubusercontent.com/10768210/86338378-ddbbd180-bc84-11ea-910d-fdac775b7ef9.png Now, I have genome fasta and annotation (gff3/gtf) files for my study species. But how to use it? By the way, through Google I know this code is writes using the Flask web framework. So, I run is with python Web/app.py after clone it. But there is a stderr with no found of BE-FF.html and give me a empty pages when open with firefox.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/RoyRabinowitz/BE-FF/issues/1#issuecomment-652890216, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANEH4A6PA4JJUY3PLB46Y33RZRFVPANCNFSM4OM4VB6A .

--

Roy Rabinowitz, PhD Student Prof. Daniel Offen's Neuroscience lab Felsenstein Medical Research Center Sackler School of Medicine Tel-Aviv University

[tiramisutes]

Ok, I will try my best as your suggestion. Thanks.