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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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CRIPRessoPooled - query #38

Closed frankbioinfo closed 6 years ago

frankbioinfo commented 6 years ago

Hello once again @lucapinello

Sorry to bug you again, I am using CrispressoPooled to analyze some pooled amplicon data

My experimental set up,

Paired end seq, 4 samples, 6 amplicons and 6 guides, i prepared the description file as mention in the docs had few questions

1) it the pooled analysis limited to only 5 amplicons? "A description file containing the amplicon sequences used to enrich regions in the genome and some additional information. In particular, this file, is a tab delimited text file with up to 5 columns (first 2 columns required):"

2) Also i see this error "Skipping amplicon [site4] since no reads are aligning to it" all the other (5 of them) amplicons produce results as expected except site4, to add further I use the this amplicon and guide and process it using (the same fastq files) only CRISPResso.py and it seems to work fine was wondering what am i missing. Note i am using default parameters for both the analysis.

Thanks a ton once again.

Frank

lucapinello commented 6 years ago
  1. Each amplicon is on a different row not columns
  2. It may be an artifact of the demultiplexing if you are amplicons are not distinct