cfRNA-SEEK

Website hosted by github page: https://lulab.github.io/cfRNA-SEEK

Scripts for cfRNA Sequencing Data Analysis

This repo contains scripts used in cfRNA-SEEK, a pipeline for identification of cancer relevant features from cfRNA sequencing (cfRNA-seq) data generated by SMART-Total protocol. Scripts for small cfRNA-seq data processing are also available. We also provide snakemake files to tidy up the scripts.

• SMART-total cfRNA-seq Reads Processing

To quantify different RNA variations for human genome, as well as the abundance of different microbial taxa, see analysis-step-smart-total-libraries.md.

• Feature Selection

To nomalize data matrix, remove batch effect, identify cancer relevant features and evaluate the classification performance, see classification.md.

• Small cfRNA-seq Reads Processing

To analyze small cfRNA-seq data, see analysis-step-small-RNA-libraries.md.

• Dependency

  program	version	purpose
  cutadapt	2.3	Trim adaptor and low quality sequence
  STAR	STAR-2.5.4a	Reads alignment
  bowtie2	2.3.5	Reads alignment
  MarkDuplicates (picard toolkit)	2.20.0	Duplication removal
  samtools	1.9	Manipulation of bam file, quanltification of editing level
  bedtools	2.28.0	Assign mapped reads to different genomic regions
  rMATs	4.0.2	Alternative splicing analysis
  featureCounts	1.6.2	Quantify gene expression
  DaPar	0.91	APA analysis
  RNAeditor	1.0	Identify RNA editing sites
  edgeR	3.24.3	Normalization and differential expression analysis
  RUVSeq	1.6.1	Normalization use control genes
  scipy	1.4.1	Perform ranksum test
  sklearn	0.22.2	Feature selection and performance evaluation
  skrebate	0.6	For SURF based feature selection
  imblearn	0.6.2	Implements a balanced random forest classifier

Illustration of cfRNA-SEEK work flow