bioinformatics_util

draft.R

This .R contains all the commonly used function for data processing and analysis in R.

plot_script

This directory contains contains examples usage fo draft.R, as well as plotting/processing script in R.

align.py

This python3 script is for aligning single/paired-ended fastq files using bowtie2, bwa, STAR and hisat2. Change the header accordingly for the path of fastqs, aliger, and slurm job details.

runMELT.py

This python3 script is for submitting individual slurm jobs Mobile Element Locator Tool(MELT) for all .bam files in a directory.

tradseq_to_repenrich2.sh

This shell script is to process fastq generated by in-house sequencing method (TRAD-Seq by Devin King devking@stanford.edu) to produce Repenrich2 output. Change the form on top accordingly for use.

extract_uml.sh

Supporting script for tradseq_to_repenrich2.sh written by Devin King.

build_signal_track2.R

Supporting script for tradseq_to_repenrich2.sh written by Devin King, partial code of the TRAD-Seq computational package.