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QoRTs Package User Manual
Stephen Hartley
National Human Genome Research Institute
National Institutes of Health
QoRTs v1.0.22
- Contents
- Overview
- Requirements
- Installation
- Preparations
- Quick Start
- Dataset Organization
- Processing of aligned RNA-Seq data
- Visualization
- Reading the QC data into R
- Generating all default plots
- Plotting by sample, lane, or group
- Description of Individual Plots
- Phred Quality Score
- GC Content
- Clipping Profile
- Cigar Op Profile
- Cigar Length Distribution
- Insert Size
- N-Rate
- Gene-Body Coverage
- Cumulative Gene Diversity
- Nucleotide Rates, by Cycle
- Aligned Nucleotide Rates, by Cycle
- Leading Clipped Nucleotide Rates
- Trailing Clipped Nucleotide Rates
- Mapping location rates
- Splice Junction Loci
- Number of Splice Junction Events
- Splice Junction Event Rates per Read-Pair
- Breakdown of Splice Junction Events
- Breakdown of Splice Junction Events, by locus type
- Strandedness test
- Mapping stats
- Chromosome counts
- Normalization Factors
- Normalization Factor Ratio
- Read drop rate
- Gene Biotype Rates
- Summary Tables
- Identifying Problems
- Secondary Utilities
- Generating a flattened annotation file
- Merging Count Data
- Generating genome browser tracks
- Importing data into other tools
- Bibliography
- Session Information
- Legal
- About this document ...
Dr Stephen William Hartley 2016-05-18