In the past, we've used an Illumina GA for our RNA-seq experiments. In general, we noticed that the reported quality of the read bases was highest at the 5' end of each read, and the quality dropped gradually towards the 3' end (as per the FASTQ files). This is what we expected.
Recently, however, we've received an RNA-seq dataset generated from a HiSeq 2000, and notice a different pattern. The 5' bases have a high quality, but the quality actually improves in the 3' direction until about base 20 (out of 90), and then drops gradually.
Can someone perhaps comment on whether this alternative pattern is just a harmless artifact of the HiSeq 2000, or if it should be a cause for concern?