FastQC results of the raw sequences from first analysis.

Analysis of the 12 FASTQ files ((2 conditions per replicate)*(3 replicates)*(2 rounds of sequencing for each sample in the paired end protocol)) produced by the HiSeq 2000 sequencer are concatenated into a single file. Each file was named by replicate and condition (for example, files beginning with 2A are the anterior fragment of replicate 2), followed by the adaptor barcode sequence used to classify the read, followed by indication of which end was sequenced (R1 is first strand, R2 is the second strand). A "failed" assessment does not necessarily mean a significant problem in the data. For example we consistently receive warnings on the "per base sequence content" analysis, but this seems to be inherent to the Illumina protocol. On the other hand, the "per tile sequence quality", and "Adapter Content" warnings were not seen previously and were cause for concern.