If even the less stringent trimming procedure engendered a matrix with fewer than 4 columns, the matrix was discarded.
It is possible these areas could have been eliminated with more stringent trimming, however, since these also occurred in areas covered by at least three contigs and the others aligned without mismatches, these bases were discarded from the assembly.
Averaging the trait measurements was not as efficient as stringent bivariate trimming.
Stringent bivariate trimming of data, using only trait values that were similar to each other in the two data sets, substantially improved the correlation of trait values and allele effects in the GWAS, and showed evidence for two QTL on BTA14 separated by 1 Mb.
The stringent approach taken here with orthology assignment of high quality contigs and rigorous trimming of the resultant alignments is therefore rather conservative, despite a considerable loss of data.
Under a more stringent procedure we trimmed the full filtered length reads (from above 40 85 nt) more robustly by trimming 10 nt from 5' end and 5 nt from 3' end of each read (25 70 nt length).
To minimize the effects of random sequencing errors and avoid overestimates of the phylogenetic diversity [ 57], relatively stringent quality-based trimming of the reads was performed.
To improve data regularity and quality, all reads were subjected to stringent length filtering and trimming (between 300 and 350 bp trimmed reads, depending on the amplicon), which resulted in the loss of 25%to60%0% of total filterpass sequences.
Nevertheless, even with the most stringent amounts of bivariate trimming, so that the trait measurements were very highly correlated, the list of significant SNP of the two GWAS did not coincide.
To maximize the relatively high accuracy of Roche GS-FLX 454 sequencing and to ensure a more accurate de novo transcriptome assembly we accepted sequences for assembly only after a stringent quality control and trimming process.
