panxiaoguang / surronprot

Some scripts including library design and read analysis for SURROseq

Welcome to SurroNPROT official repository!

MainScripts

This is a directory that contains all scripts used in the SurroNPROT protocol. please find them in the directory: MainScripts/

Scripts for library design

• on-target_design.jl: This script is used to design on-target SURRO_seq library for given regions of sgRNA.
• utils/find_locations.jl: This script is used to find the locations of given sgRNAs in the genome by alignment(bwa).
• off-target_Artificial_design.jl: This script is used to design off-target random mismatches library for given on-target sgRNA regions( get location by find_locations.jl).
• off-target_genome_design.jl: This script is used to design off-target SURRO_seq library for given on-target sgRNAs.
• off-target_PAM_design.jl : This script is used to design off-target random PAM only library for given on-target sgRNA regions( get location by find_locations.jl).
• utils/remove_BsmBI.jl: This script is used to remove BsmBI restriction enzyme sites in the designed library.

Scripts for library analysis

• get_seq.py : This script is used to get the sequences(or we can call it library seperation) according to desgined library.
• remove_synthesis_error.jl: This script is used to remove synthesis error.
• get_indel_profile.jl: This script is used to get indel profile.
• remove_sequencing_error.jl: This script is used to remove sequencing error and get the final indel counts.

One-key workflow

We also provide a one-key workflow for the whole SurroNPROT protocol. Please find it in the directory: WorkFlow/ It is a snakemake workflow, and you can run it by the following command:

cd WorkFlow/
snakemake -s SurroNPROT.smk --cores 10 --use-singularity --singularity-args "--cleanenv --no-home"

You should prepare your input fasta files and put them in the directory: WorkFlow/rawData/ and modify the WorkFlow/config/samples.tsv according to the example file as well as the WorkFlow/config/config.yaml file.

You can also have a peek at the example report created by this workflow based on example data in this link: preview

We also provide an example input file in rawData/ dir and the corresponding configuration file in config/ dir. If your would like to try the example input, please delete all directories except rawData/, config/ /references /scripts/. Of course, the two files SurroNPROT.smk and util.py should be kept as well.

Dependencies (Singularity container)

Please download all softwares for this pipeline in this link: