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Big Data and Transcriptomics
Published in Shampa Sen, Leonid Datta, Sayak Mitra, Machine Learning and IoT, 2018
Sudharsana Sundarrajan, Sajitha Lulu, Mohanapriya Arumugam
The raw sequence-based metrics checks the experiments at low-level as prior sequence alignments are not required. The raw sequence quality is assessed based on the Phred quality score (Q). Phred score measures the base-calling reliability from Sanger sequencing chromatograms. It is defined as Q = −10 × log10(P), where P is the probability of erroneous base calling. GC content gives the percentage of either guanine or cytosine bases in a DNA sequence. It is a simple way to measure the nucleotide composition. Read duplication is often determined by read length, transcript abundance, PCR amplification, and sequence depth.
Contrasting histories of microcystin-producing cyanobacteria in two temperate lakes as inferred from quantitative sediment DNA analyses
Published in Lake and Reservoir Management, 2019
Shinjini Pilon, Arthur Zastepa, Zofia E. Taranu, Irene Gregory-Eaves, Marianne Racine, Jules M. Blais, Alexandre J. Poulain, Frances R. Pick
Initial data trimming of the sequence data was performed using the program MOTHUR (v. 1.33.3; Schloss et al. 2009). The quality file was used to eliminate sequences with an average Phred quality score below 25. Low-quality sequences (length less than 100 and over 1000 bp) were removed, as well as sequences with ambiguous bases. Remaining sequences were then aligned using Silva reference files, and chimeras were subsequently removed using Chimera Slayer (Haas et al. 2011). Sequences representative of cyanobacteria were identified using the online Ribosomal Database Project (RDP) classifier, which is specifically designed for classifying bacterial 16S rRNA sequences (Wang et al. 2007; Cole et al. 2014). Sequences not identified as cyanobacterial by the RDP classifier were removed from further analyses. Previous studies have found non-cyanobacterial species amplified using cyanobacterial-specific primers and have similarly filtered them out of downstream analyses (Kleinteich et al. 2014).