| For the final scoring of the junctions all of the developmental RNA-Seq data was aligned to a bowtie index containing both the genome and the 79,514 splice junctions. For single reads, the alignments were performed with the following parameters to report uniquely mapped reads [-m 1 -v 2 -y --best]. For paired-end reads, the data was aligned using the following parameters [-m 10 -v 10 -y --best] after which spa was used to to identify unique instances of mate-pairs in which both reads map on the same chromosome, within 200 kb of one another and oriented towards one another. The remaining reads were further filtered to identify cases in which there were multiple potential mapping positions of a mate pair within 200 kb of one another. In this case, the closest of multiple mate pair mapping positions was retained. Finally, for mate pairs in which only one read could be mapped, if the remaining read was mapped uniquely, it was retained. Junctions were scored using both the total number of reads and the entropy score. |
