If you used the raw illumina fastq data (the txt file generated) file that 
means that your data quality is very low, the sample has been most likely 
contaminated.

you can still run it just to see what it gives you.

Best of luck

Kreshnik
On Mar 28, 2013, at 9:41 AM, "Tan, Justin" 
<j...@fas.harvard.edu<mailto:j...@fas.harvard.edu>>
 wrote:

Hi,

I am having a problem with FastQC. When I view per base quality, it gives me a 
strange looking graph:
<per_base_quality.png>


I am wondering it this is because of a problem with my data? None of my 
colleagues have seen this before.

Thanks!
Justin



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