Data analysis flow-chart. RNA-Seq reads are aligned to the genome using Bowtie to generate a single nucleotide resolution map. Mapped reads analyzed in the context of existing annotation using SAMTools and Perl scripts generate expressed intergenic regions (EIRs). Homologs for EIRs, if present, are identified by BLASTX and are classified accordingly. An EIR with no BLASTX matches is subjected to computational search for regulatory elements (promoter/rho-independent terminator) in its vicinity. An EIR with a regulatory signal is classified as potential sRNA. EIR without BLASTX matches and predicted transcriptional signals are searched against Rfam database.
Reddy et al. BMC Bioinformatics 2012 13(Suppl 15):S4 doi:10.1186/1471-2105-13-S15-S4