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Old 03-09-2016, 11:58 PM   #1
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Location: China

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Unhappy what's wrong with the pair-end seq data if the fastqc report shows this patten?

I fsatqc the uniq-mapped reads, and the "Kmer content" showed a high repeat "CCCTACGTTCT" at the middle of the reads.

Is this means the error in the sequencing process?
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Old 03-10-2016, 12:13 AM   #2
Devon Ryan
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Most likely, you just have a single sequence that's really really highly expressed. FastQC only shows 6 kmers in these sorts of graphs, so odds are good that there are other (not displayed) similarly enriched kmers on either side.

Alternatively, perhaps you were doing RIPseq and this is a binding motif (the fastQC results on such experiments looks similar).
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Old 03-10-2016, 02:57 AM   #3
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There seems to be something concatenated. Note the same order of peaks (red, green, black, blue, pink) in the middle and at the end of the sequence reads.

What are these data? Since they seem to be only 45 bp in length they are probably not freshly sequenced?!

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