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Old 02-24-2015, 05:01 AM   #3
Location: Portugal

Join Date: Nov 2010
Posts: 11

Thanks for the reply

Yes. Running w/out the "--casava" option was the first thing that I did. However, I got some weird Kmer profiles. FASTQC doesn't detect any adapter content / overrepresented sequences but it shows Kmer enrichments around the center and towards the end of the read...(I am attaching one example)

I have limited experience with NGS data so I have no idea whether this has anything to do with the way I am "using" the data. The pattern is actually similar for most fastq.gz files so perhaps this is a problem with the data itself.
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