RNAtag-seq and term-seq samples of E. coli K12 MG1655 cells grown to exponential phase in rich and minimal media.

In this study we developed TRS, a computational approach to determine the 3' termini of transcripts from total RNA data generated by the RNAtag-seq protocol. To show the applicability of our approach, we applied our algorithm to sequencing data generated by the RNAtag-seq and the term-seq protocols. In term-seq, a 3' adaptor is ligated to the RNA 3' termini prior to the RNA fragmentation, and thus, the sequences adjacent to the adapter sequence in the library reads represent original 3' termini that were present in the RNA sample. The RNAtag-seq protocol involves ligation of a 3' adaptor after the RNA fragmentation and thus, the sequences adjacent to the adapter sequence in the library reads represent genuine 3' termini that were present in the RNA sample and artificial 3' termini generated by the RNA fragmentation. We show that our computational approach can reliably identify genuine 3' termini from RNAtag-seq data by comparing the set of identified 3' termini based on the RNAtag-seq and the term-seq protocols.