Abbreviations

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Alex H. Wagner, PhD edited this page Nov 13, 2017 · 11 revisions

7-ii. 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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NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.

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