To remove sequencing errors, chimeric reads were identified and removed using ChimeraSlayer with default settings.
For example, mothur included a single linkage preclustering module to merge similar sequences before clustering (Schloss et al., 2009), and PyroNoise (Quince et al., 2009) was developed to remove sequencing errors to alleviate the overestimation of the number of OTUs.
As described in the Methods Section, we devised a method based on comparing relative read abundance of parent and variant sequences in order to remove sequencing errors from our dataset.
Using a large k-mer has the advantage of resolving more repeat regions; whereas, use of small k-mers is advantageous for assembling low coverage depth and removing sequencing errors.
The choice of data pre-treatment technique, in which data are pre-processed to remove sequencing errors and other artefacts, influences the accuracy and precision of the gene expression analyses [ 19].
These reads were processed by AmpliconNoise (Quince et al., 2011), which attempts to remove sequencing error and generates a set of predicted sequences for the amplicons.
Even after the raw output was pared back to genuine sites of interest, JSM2's candidates had the lowest pass rate through filters to remove sequencing error and then after that were found to have 50% constituency in dbSNP.
The techniques used to remove sequence errors and correct relevant artefacts can be found in [ 10, 11], and [ 15].
In many cases the initiation and/or stop codons could not be accurately identified because of a lack of overlapping clones to remove sequence errors or a lack of clones representing full length cDNA products.
Rather than reducing the number of candidates by increasing the probability score threshold for inclusion, we applied filters designed to remove sequencing and mapping errors.
