Base editor design tool

This code designs every possible guide in the CDS region, 30 nucleotides into the intronic and UTR regions for user-defined transcripts. It then annotates the possible edits for each guide. Separate files annotating ClinVar SNPs are also generated.

Author: Mudra Hegde, Ruth Hanna
Email: mhegde@broadinstitute.org, rhanna@broadinstitute.org
Version: 2.0

Inputs

1. Input File:.txt file with list of Ensembl transcript IDs in the first column and gene symbols in the second column OR FASTA file with nucleotide sequence
2. Variant File: Variant file: File with ClinVar SNPs (variant_summary.txt). This file can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz.
3. Input type: Indicate whether the file contains a list of transcripts or a nucleotide sequence.
4. Base editor type: Indicate the type of base editor (Rees et al.,2018) for which designs are required. This choice dictates the choice of PAM, sgRNA length, editing window and type of edit.
5. PAM: PAM preference if BE type has not been selected; Default: NGG.
6. Edit window: Editing window relative to nucleotide position in sgRNA, if BE type has not been selected; Default: 4-8.
7. sgRNA length: Length of sgRNA excluding PAM sequence, if BE type has not been selected; Default:20.
8. Edit: Type of edit made by base editor, if BE type has not been selected; Default: all, annotates for both C->T and A->G edit.
9. Intron buffer: Number of bp into the intron to consider for guide design.
10. Filter GC: Whether to filter out edits in a GC motif.
11. Output name: Name for output folder.