PreAlignment QC

#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://cshl##.dyndns.org/workspace/rnaseq/data/
• right-click to save a fastq file to your laptop
• Note, you must replace cshl** with your own amazon instance number (e.g., "cshl01"))

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