Identification of PASs using orthologous transcripts and total RNA sequencing data. Panel A. Genomic context of a putative PAS associated with a TransMap transcript (Trans). The last two exons (and the last intron) of the Ensembl prediction that could have a larger associated isoform using the putative PAS are shown above (Ensembl). The TransMap transcript and total RNA Seq coverage for the interval is shown below. The intervals used to calculate the Coverage Difference (CD) and the applied formula are indicated. Up, upstream interval; Down, downstream interval. Panel B. FDR values calculated using each of the putative PASs CD as a cutoff. The putative PASs were obtained using the Ensembl database as reference and were ranked according to their CD. The one with the highest CD is on the first position of the scale, the putative PASs with the second highest CD is on the second position, and so on until the last position with the putative PASs with lowest CD. The FDRs obtained using as cutoffs CDs of 95, 80 and 50 are indicated. The numbers of putative PASs with a CD equal or higher than the cutoff used are shown between brackets. Panel C. As in B using the RefSeq database as reference to obtain the putative PASs.
Morgan et al. BMC Genomics 2012 13:708 doi:10.1186/1471-2164-13-708