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" <jtan@fas.harvard.edu<mailto:jtan@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/