The Environmental Protection Agency will begin taking samples of the sludge and floodwater this week to check for contaminants, city officials said.
The resulting trimmed reads were checked for contaminants, and low quality bases and contaminants were removed using the cutadapt software (Martin 2011).
Raw fastQ files were checked for contaminants and low-quality bases and contaminants were removed with the cutadapt software [ 103].
We also noted that when both libraries were checked for contamination by WSSV sequence, 167 ESTs were found to be WSSV contaminants in the PmTwI library (E value < 10-25, score > 100), whereas there were no WSSV contaminants in PmTwN.
All cultures were vouchered by rigorous microscopical examinination on a Zeiss Axioskop 2 Plus under the 10×dry differential interference contrast (DIC) and bright field (BF), 40×dry (DIC/Phase contrast (PC)), and 63×oil (DIC) to verify the proper taxon identification of each organism, and to check for possible contaminants.
The raw reads (100 bases, single-end) obtained from Illumina HIseq (FASTERIS Co. Geneva, Switzerland) were filtered (Illumina passed-filter call) and further checked for sequence contaminants with the fastQC application.
Plants of T. pellucida are small and sometimes grow mixed with other organisms, thus single shoots were separated under the dissecting microscope over several days with each shoot checked individually for identity and for contaminants visible at 40× magnification.
Sequences were blasted against the GenBank protein database (blastx), to check for potential bacterial contaminants.
Conventional samples were also analysed in order to check for PCR and/or seed contaminants.
Conventional samples were also analyzed in order to check for PCR and/or seed contaminants.
