Abbreviations

Jump to bottom

Obi Griffith edited this page Nov 13, 2016 · 1 revision

#5-i. Abbreviations

AWS EC2: Amazon Web Services, Elastic Compute
BAM: Binary Sequence Alignment/Map
BED: Browser Extensible Data
CIGAR: Compact Idiosyncratic Gapped Alignment Report
DNA: Deoxyribonucleic Acid
FPKM: Fragments Per Kilobase Of Exon Per Million Fragments Mapped
FPM: Fragments Per Million Fragments Mapped
GFF: Generic Feature Format
GTF: Gene Transfer Format
IGB: Integrated Genome Browser
IGV: Integrative Genome Viewer
PCA: Principal Component Analysis
polyA: Polyadenylation
QC: Quality Control
qPCR: Quantitative Polymerase Chain Reaction
RNA: Ribonucleic acid
RPKM: Reads Per Kilobase Of Exon Per Million Fragments Mapped
RPM: Reads Per Million Fragments Mapped
RT-PCR: Reverse Transcription Polymerase Chain Reaction

| Previous Section | This Section | Next Section | |:------------------------------:|:-------------------------------:|:-------------------------:| | Kallisto | Abbreviations | Lectures |

##Note: The current version of this tutorial is now at www.rnaseq.wiki

Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 5: Kallisto
Appendix: Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup