Changes between Version 3 and Version 4 of SOP/PooledCRISPR


Ignore:
Timestamp:
03/14/19 13:25:14 (6 years ago)
Author:
gbell
Comment:

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  • SOP/PooledCRISPR

    v3 v4  
    3939
    4040To identify cell line-specific essential genes, the CS distribution of each line was mean-normalized to zero. For each gene in each line, the CS in the given line was subtracted by the minimum CS in the other three lines to define a cell line-specific essentiality score (negative values indicate cell line specificity). For each line, genes with a differential score less than -1.5 (~4 standard deviations from the mean score) whose minimum CS in the other three lines was greater than -1 were defined as cell line-specific genes.
     41
     42== Getting guide counts from reads ==
     43
     44'''Implementation 1: alignment free'''
     45
     46* Read in list of CRISPR guide sequences (of length n).
     47* Read through short reads, counting presence of first n nucleotides (where n can have more than one value).
     48* Iterate through CRISPR guide sequences, printing counts for each one.
     49* Also print out most prevalent n-mers that are not in CRISPR guide list (for quality control).
     50* See /nfs/BaRC_Public/BaRC_code/Perl/read_count_CRISPR_guides for this implementation.
     51
     52'''Implementation 2: using bowtie alignment'''
     53
     54