Abbreviations

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Obi Griffith edited this page Mar 18, 2017 · 11 revisions

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

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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: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup