Table 1.
Summary of genomic, cDNA, exon junctions, splice leaders, and polyadenylation site alignments from constructed libraries
Libraries were constructed using the dsDNALigSeq, ssRNALigSeq, and CircLigSeq methods. The sequence tags were collapsed (multiple incidents of the same tag were considered only once such that the read count and tag counts are identical) and aligned to a WS190 cDNA library using MAQ. Sequence tags that did not align to the cDNA library were aligned to the WS190 genome, and the aligned sequences were considered as nonannotated genomic tags. The remaining sequences were aligned to the putative exon-junction databases to identify nonannotated splice junctions or were used to identify polyadenylation sites or splice leaders (SL1 and SL2). mRNA coverage was calculated by the number of bases in each tag times the number of annotated cDNA tags in each sample divided by the estimated WS190 cDNA size (about 25 million bases).