berets 0.1.2

Tools for analyzing CRISPR data with REPorter edits

Base Editing with Reporter analysis Toolkit.
This is an analysis toolkit for the pooled CRISPR reporter or sensor data. The reporter technique transfects cells with plasmid with not only sgRNA but with the target sequence surrogate which we call reporter or sensor.

Installation

Downloading from PyPI:

pip install berets

Count reporter screen data

Aligns guide with matched reporter allele counts in multiple samples.

beret-count-samples         \
  --input sample_list.csv   \ # sample with lines 'R1_filepath,R2_filepath,sample_name\n'  
  -b A                      \ # base that is being edited (A/G)
  -f gRNA_library.csv       \ # sgRNA information 
  -o .                      \ # output directory    
  -a                        \ # read allele information  
  -r                        \ # read reporter edit information
  -m                        \ # read matched guide and reporter edit information  
  -t 12                     \ # number of threads  
  --name LDLvar_fullsort    \ # name of this sample run  

This produces .h5ad and .xlsx file with guide and per-guide allele counts.
.h5ad file follows annotated matrix format compatible with AnnData and is based on Screen object in purturb_tools and contains the per-guide allele counts.

Using as python module

import beret as br
cdata = br.read_h5ad("beret_counts_sample.h5ad")

See the tutorial for more detail.