fastqc kmer content error

btaboada · 08-12-2013, 03:38 PM

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!

MeganS · 08-13-2013, 10:27 AM

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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08-13-2013, 10:27 AM	#2
MeganS Member Location: US Join Date: Sep 2010 Posts: 14	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.