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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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Frozen at 91% #62

Open acuadros1 opened 4 years ago

acuadros1 commented 4 years ago

I have been trying for the past 2 days to troubleshoot an issue with the analysis tool. It is constantly stuck at 91% and "generating Fastq quality report" for several hours. I uploaded a cutom Fasta file for a subpool library made. The format for the entries are genename_seq (i.e. Tim20GACCATCGTGACTGGATCGT) so I input the custom regular expression: ^(.+?)(.*)$ My raw data was uploaded as fastq.gz compressed files. The vector used was a lentiguide Puro and all my sequences have the "CACCG-20nt sgRNA-GTTTT" motif. Since the default LGPuro regular expressions are ACC(.{20,21})G I have used a custom expression: ACCG(.{20})G Still the program hangs at 91% for several hours. Any fixes for this you have experienced? Thanks in advance.

jwinter6 commented 4 years ago

Hi, could you drop me some fasta/fastq files (or parts of it)?

Best, Jan

acuadros1 commented 4 years ago

Hi Jan,

I have it working now I just started from read counts instead.

Best, Alex Cuadros

On 21 May 2020, at 17:15, Jan Winter notifications@github.com wrote:



Hi, could you drop me some fasta/fastq files (or parts of it)?

Best, Jan

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afaissa commented 3 years ago

Hi,

Thanks for the package, but I have the same problem here. Using four fastq files (~1GB each) didn´t pass the first step. If I upload only two, it works on the first step but it stops on 9% on the the "Check Gene and sgRNA Readcount for consistency".

It is running for 4 hours and there is no error message, though.

Best,