PreAlignment QC

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Malachi Griffith edited this page Apr 27, 2015 · 41 revisions

RNA-seq Flowchart - Module 2

#2-vi. Pre-Alignment QC

You can use FastQC to get a sense of your data quality before alignment:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Video Tutorial here:

http://www.youtube.com/watch?v=bz93ReOv87Y

Try to run FastQC on one of your fastq files

Go to the following url in your browser:

http://cbw##.entrydns.org/workspace/rnaseq/data/
right-click to save a fastq file to your laptop
Note, you must replace cbw## with your own amazon instance number (e.g., "cbw01"))

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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