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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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CRISPRessoCount #71

Closed BeyondMyPast228 closed 3 years ago

BeyondMyPast228 commented 3 years ago

Hi， Thanks for developing this user-friendly tool. In your first edition, CRISPRessoCount is a utility for the enumeration of sgRNA. But in CRISPResso2, I did not find any function that could help me count the number of sgRNA. I don't know whether there is a new improvement or the removal of this function. In order to count the number of sgRNA in my plasmid, I used the CRISPRessoCount in the old version. Unfortunately, i met some problems. The first problems is that input fastq file does not support double-ended sequencing. The second problems is that outcome is always zero value. just like the below picture. image My sgRNA file is: image my fastq file is: image My code is: CRISPRessoCount -r 0124-A_FKDL202628179-1a_1.fastq.gz -s 20 -q 30 -f 0124a.xlsx -l 20 -n 0124A I sincerely hope to get your help. Thanks

BeyondMyPast228 commented 3 years ago

I'm sorry I can't upload the picture, Could you please send me your email? I will send some data to you for testing.

kclem commented 3 years ago

Hi @BeyondMyPast228,

Thanks for using CRISPResso. We don't really have support for CRISPRessoCount in CRISPResso2 at this time. If you'd like to set up a formal collaboration to revisit it, you can let me know at kclement@mgh.harvard.edu.