Dear all,

I'm analyzing eukaryotic metatranscriptomics HiSeq (2x100 bp) data from soil (the cDNAs are from eukaryotic poly-A mRNAs). The FastQC report of the R1 reads shows that there is a sudden sequence quality drop around the 50th nucleotide, even some unknown bases (Ns), and high Kmer content (see [here][1]). However, this drop in quality and unknown bases are absent in the R2 reads ([there][2]).

I wonder if it is normal to have something like this, and if it is not, what should I do to improve the read quality?

 [1]: https://drive.google.com/file/d/0B1HJ6hkNttmvY3VLR1A4SlBVSk0/view?usp=sharing
 [2]: https://drive.google.com/file/d/0B1HJ6hkNttmvU05HbTNrczFOSXc/view?usp=sharing
<p>This is likely due to a bubble going through as the image was being acquired. This actually used to be fairly common. Whether this will be an issue or not will depend a bit on exactly what you want to do with the data.</p>
