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Old 08-12-2013, 02:38 PM   #1
btaboada
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Location: Mexico

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Default fastqc kmer content error

Hello,

I have 4 different samples and in all of them I got some weird peaks along the sequences in FastQC kmer content graphics (plz see the attached graphs). I would appreciate it very much if anyone has a clue of what is happened in my data set. Many thanks!
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File Type: png kmer_profiles_1.png (128.8 KB, 42 views)
File Type: png kmer_profiles_2.png (130.1 KB, 17 views)
File Type: png kmer_profiles_3.png (97.3 KB, 16 views)
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Old 08-13-2013, 09:27 AM   #2
MeganS
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What type of samples are these(whole genome, transcriptome, RAD, etc.)? It could be contamination of some sort. You can tile the kmers together to get a longer sequence (TATCCTCCAGTG). I would compare that sequence to your adapters, primers, and other possible sources of contamination. I would also check and see how many reads this is actually affecting.
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