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Old 11-16-2016, 10:48 AM   #2
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Join Date: Feb 2008
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I am not familiar with MNase-seq but perhaps that enriches some sequence that may be leading to that particular enrichment of k-mers.

Different criteria (pass/fail) used by FastQC are settings that can be changed and are configured (default) for normal genomic sequencing. Any experiment that deviates from the norm is likely to generate some fail flags. That does not automatically make your data bad. You should keep those observations in mind as you proceed with your analysis. If you are unable to get reasonable alignments then you can circle back and check if these k-mers are responsible for it.

The string of poly G's is a characteristic of NextSeq data. NextSeq uses a 2-color chemistry so absence of any signal is considered a G. See this link. You can trim those reads out using GGGGG as seed for the trimming program.

Last edited by GenoMax; 11-16-2016 at 10:50 AM.
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