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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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Running CRISPResso - query #22

Closed frankbioinfo closed 6 years ago

frankbioinfo commented 6 years ago

hello Developer,

Thank you for developing this tool.

I am not sure which module should I use for my purpose, we have crispr guided to a target region. we then sequenced the genomic dna (pcr product) that targets this region using miseq 2x250 + 10bp Index1 + 8bp Index2 I used two two different approach

  1. using fastq and
  2. using the bam file (alignment using bwa)

I have attached plots from both the steps, having difficulty in understanding the plots. could you please help in this?

4b.usingbam.pdf 4b.usingfastq.pdf

lucapinello commented 6 years ago

We don't support reads aligned through BWA so I am not sure what I am looking at. You should use CRISPResso with paired end reads in fastq format. I suggest you to read carefully the paper (http://rdcu.be/jgvL) and supplementary material: https://www.readcube.com/articles/supplement?doi=10.1038%2Fnbt.3583&index=0&ssl=1&st=f5e8a734a3bfafe4c31a97f8993f72d1&preview=1 where we explain in detail the required inputs, parameters and the different tools.

The plot 4b.usingbam.pdf looks more reasonable to me.

Regards,

Luca