ePyGenetics-Tools

• This is a collection of scripts I use for molecular biology.

sgRNA tools

1. RevComp: biopython wrapper script that allows the user to input a short nucleotide sequence and outputs the reverse complement of the sequence.
2. GuideToOligo: takes a list of 20-bp sgRNA sequences and ouputs a list of cloning ready oligos for each. Also utilizes biopython.
3. get_reverse_complements.ipynb: this jupyter notebook has a few python scripts for outputting reverse complemented oligo tables.
4. retrieving sgRNAs from library: this is a markdown file with my instructions for retrieving a set of sgRNAs from a library and formatting them into order-ready oligos.
5. ChopDatUp: breaks sequences larger than 2kb into smaller chunks for submitting to CRISPick. Run using following command: python ChopDatUp.v5.py <path to input files> <path to output files>.

Oxford Nanopore Sequencing tools

1. make.tar.sh and make.merged.fastq.sh: these scripts respectively tarball ONT minibam files and merge ONT minifastq files. the instructions are contained in the maketar_makemergedfastq.instructions.md file.
2. babam.md: draft of a script collection for creating merged bam files from ONT minibam files, aka big-a** bam files (BA-BAM files). UPDATE: Deprecated. Please use the master script babam.sh instead, see below.

Pipelines

1. make.PE.chip.scripts.sh: generates individual shell scripts for QC, trimming, alignment, bigwig track generation and upload. Usage: make.PE.chip.scripts.sh -w <workDir> -f <fastqDir> -g <genome> -s <scientistID> -t <tangoNumber> [-r <runflag: 0 or 1>]. Note that this assumes the _SXX_R1_001.fastq.gz naming convention for fastq files. Modify accordingly if not the case. Spike-in version is being tested.
2. babam.sh: generates sequential merge scripts for minibam files generated during ONT sequencing. Usage: bash babam.sh $0 -m <text file with absolute paths to minibam files> -w <absolute path to working directory> -r <1|0 user run flag>. In progress!