This repository contains the code used in "CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments" by Lindsay et al.
This repository also contains the Sanger sequencing data from Burger et al referred to in the paper. Other data used in the paper is publically available. See the pdf for further details of where the data can be assessed and how these scripts are used.
In addition to several freely available software packages described in the pdf document, this code relies on the following scripts being in the src directory:
- [psl2sam.pl] (https://github.com/samtools/samtools/blob/develop/misc/psl2sam.pl) is part of the samtools suite.
- samGetSEQfast.pl from the rackJ toolkit.
We also include a script
- ampliconDIV_minimal.sh in the src directory, which we run from the ampliconDIVider directory. This code is an excerpt from the ampliconDIVider_driver.sh, written by Matthew LaFave (https://github.com/mlafave/ampliconDIVider).
- CRISPResso_pooled_layout.txt contains the commands used for running CRISPRessoPooled. The matching script is src/run_crispresso_pooled.sh
- shah_custom_amplicons.txt contains the custom amplicon sequences inferred from the differences from the mapped sequences to the danRer7 reference, which was used for running CRISPResso.
The following files refer to data from "Rapid reverse genetic screening using CRISPR in zebrafish" by Shah et al:
- shah_guides.bed - the locations of the guides in the danRer7/Zv9 genome.
- shah_primers.bed - the range spanned by the PCR primers, i.e. the amplicon ranges
- shah_fwd_primers.txt - the guide names and corresponding forward primer sequences
- Shah_metadata_edited.txt - this is an edited copy of the original metadata table from Shah et al with a small transposition error corrected.
- Shah_cut_sites.txt - the locations of the cut sites in the danRer7/Zv9 genome.
The following files refer to Sanger sequencing data from Burger et al:
- Burger_Sanger_guides.bed
- Burger_Sanger_metadata.xls
- Burger_wtx_metadata.xls
The following files refer to MiSeq sequencing data from Burger et al:
- Burger_MiSeq_guides.bed - this file gives the locations in danRer7 of all guides used in the Burger et al MiSeq sequencing experiment.
- Burger_MiSeq_layout.txt - In Burger et al, some PCR primers were used for multiple guides. This file gives the primer names, the guide names, and the samples the guide occurs in.
- Burger_MiSeq_primer_ranges.bed - this file gives the locations of the PCR primers used in the Burger et al MiSeq sequencing experiment.
Finally, the following is a copy of the metadata table from Cho et al with some minor reformatting:
- Cho_Table2_reformatted.xls