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Clean reads were produced by excluding reads smaller than 18 nt and adaptors.
After excluding reads that had a match to more than 20 WGS reads, we retained 18868 reads (4959 unique reads).
After excluding reads smaller than 18 nt and adaptors, approximately 88% of clean reads were analyzed (Additional file 6).
We filtered Illumina reads by converting bases with Phred quality scores less than 20 to missing (N), and excluding reads with fewer than 75 high-quality (≥20) bases.
After removing additional fungal and bacterial sequences, and excluding reads shorter than 50 nt, 2.76 × 10 sequences were available to assemble the reference transcriptome (Table 2).
The latter was done measuring the linguistic complexity [ 66] of the sequences in 16 bp windows, and excluding reads with an average complexity of less than 0.75.
Out of 685,411 unique clean reads (excluding reads with low quality and mapped to known house-keeping noncoding RNAs), representing ~11.8 million of raw reads, 55.2% (378,597) and 56.5% (387,518) were mapped to tobacco ESTs and GSSs, respectively.
We removed chimeric read pairs by excluding read pairs if one or two ends were found in the middle of the contig, but the edge length was larger than the insert size.
A total of 377,328,013 reads represented by 27,318,558 unique sequences were perfectly mapped to the V. vinifera PN40024 reference genome [ 1], excluding reads mapping to rRNA, tRNA, snRNA, and snoRNA sequences.
