Tools for analyzing CRISPR data with REPorter edits
Project description
beret
Tool for analyzing CRISPR data with reporter edit counts.
Installation
Clone and do
pip install -e .
Count reporter screen data
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_info/LDLvar_gRNA_beret.csv \ # sgRNA information
-n sample \ # number of sample
-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 120821_LDLvar_fullsort \ # name of this sample run
This produces .h5ad
and .xlsx
file.
Analysis
adata.log_norm
adata.log_fold_change_aggregate("bot", "top")
Using as python module
import beret as br
cdata = br.read_h5ad("beret_counts_sample.h5ad")
See the tutorial for more detail.
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