Hi, apologies for this basic question as I am new to the field. I have been checking my NGS data using FastQC and the checks fail on the Kmer content section. There appears to be a sequence TAGATCGGAA at position 90-100 bp in the reads which is enriched around 12 fold (Obs/Exp Max). However nothing shows up in the 'Overrepresented sequences' or 'Adapter content' sections of the report (complete flat line). The sequencing was done as BGI and I do not know what primers were used. My question is should I be trying to remove this Kmer sequence?

<img alt="screenshot" src="http://i483.photobucket.com/albums/rr194/Kez_Cleal/Screen%20Shot%202015-05-28%20at%2013.11.25_zpsagvhw2h3.png" style="height:50%; width:50%" />

If I use grep on the first million reads in my fastq file to look for the sequence I only find 36 which appears to be quite a low number?

    $ gunzip -c data1.fq.gz | head -4000000 | grep TAGATCGGAA | wc -l

Thanks for the help
FastQC often displays failed checks - it does not mean your data is bad, they are just warnings.

The only thing you should always really check is the quality along the length of your reads, which might force you to do some trimming. In this case, I would say that your reads are ok as they are, and you can proceed to the alignment phase of your workflow.