This repositroy is for transcriptional stress study including the code (custom and public) and processing data with instruction.
Each code and their corresponding outcome can be found in folder followed by the paper stucture. The extra inputs required from the custome codes and public softwares can be found in the "reference folder" with the following description:
Data processing:
Fastqc QC and alignment
Fastqc See more https://github.com/s-andrews/FastQC.
Trimmomatic See more https://github.com/usadellab/Trimmomatic.
Tophat See more https://github.com/DaehwanKimLab/tophat.
bam processing and flaging:
bamCoverage https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
Samtools http://www.htslib.org/doc/samtools-index.html
samtools flags http://www.htslib.org/doc/1.11/samtools-flags.html
Feature Quantification:
Read_distrubition.py, input: bam file, gtf/gff/bed. See more http://rseqc.sourceforge.net/#genebody-coverage-py.
HTseq-count.py, input bam files, gtf/gff/bed. See more https://github.com/simon-anders/htseq.
Travel_Ratio.r visilzation R code for plotting the scatter plot using ggplot package. See more in https://ggplot2.tidyverse.org/.
K-bining.py, input bam/bw file, gtf/gff/bed. See more http://rseqc.sourceforge.net/#genebody-coverage-py.
HOMER input bam/bw file,gtf/gff/bed. See more http://homer.ucsd.edu/homer/