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boutroslab / CRISPRAnalyzeR

CRISPRAnalyzeR: interactive analysis, annotation and documentation of pooled CRISPR screens
GNU General Public License v2.0
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Brie Library Fasta "repeated guides" #28

Closed Kevbot8000 closed 7 years ago

Kevbot8000 commented 7 years ago

Hi,

I have tried to analyze my CRISPR data a few times using CRISPR Anlyzer version 1.14, 1.17 and 1.2 but all of these versions say that the uploaded Brie FASTA file has a duplicate sgRNA identifier in the sgRNA library file. Is there an issue with the brie library fasta file that was used in version 1.2? Is this the same file that was uploaded in the GitHub page? The program looks extremely user friendly and promising- I am hopeful there is a simple fix!

Thanks!

jwinter6 commented 7 years ago

Hi,

thanks for your comment. Did you use the preset FASTA file (Version 1.20 and higher) or the one downloaded from this repository? As I do not have Brie Sequencing Data on hands, I can just try the FASTA file that I provide within this repository, and for this one there is no message about repeated guides.

Please give the following FASTA file a try:

https://github.com/boutroslab/CRISPRAnalyzeR/blob/master/fasta/FASTA_Brie.fasta

In case you use CRISPRAnalyzeR 1.20 and higher, you can directly select the Brie preset or alternatively use the CUSTOM setting and upload the above linked FASTA file.

Please give it a try and post a screenshot in case the error message appears again. Please also send me a screenshot about the setting on the Upload Data page. If you want to keep this information private, please send me an email to jan.winter@dkfz-heidelberg.de.

Thanks for your help :)

Best, Jan

jwinter6 commented 7 years ago

Just for followup for others (via email):

Ok so I found the issue, this is something related to having majority of zeroes and failing to perform DESeq2-based normalization. I will fix the confusing error message to the correct one, sorry for this.

Best Jan