In this study, we further analyzed the RefSeq associated reads.
Some genes had more associated reads than other genes.
Instead, the purpose is to eliminate the likely false alleles and their associated reads.
The selection effectively eliminates a large number of the false alleles and their associated reads that are likely unreliable.
At the end of the selection, we only include the candidate alleles and their associated reads for the subsequent analysis.
The relative arm usage was calculated as a ratio of the 5'- to the 3'-arm associated reads of the hairpin precursor and shown as log values.
The barcode sequences, number of associated reads, and the experimental description matching each barcode are shown in Additional file 1: Table S1.
To determine coverage levels for individual published E. balteatus genes, associated reads of the maternal and zygotic library sequences were identified by BLAST search (blastn) and assembled with the published sequence using CAP3 with standard parameters [ 69].
All contigs matching to the WSSV genome were isolated and associated reads were reassembled with more stringent parameters (MIRA: --job=denovo,est,accurate,454), yielding 918 contigs with 15 of them exceeding 5 kbp.
