Pipeline for predicting novel lncRNAs. (a) Initial assembly. Raw reads are first mapped onto the reference mouse genome. The un-mapped reads are trimmed before re-mapping. Merging the read alignments of all 6 replicates is to increase the read coverage. At the assembly stage, RABT generates synthetic reads from the RefSeq gene annotation to compensate the read coverage gaps over transcripts; (b) Novel lncRNAs detection. The initial assemblies are categorized by cuffcompare, compared with the combined gene annotations. The low-quality transcripts are then filtered according to the optimum FPKM (2.12). The lncRScan program is performed to detect the novel lncRNAs from the remaining high-quality assemblies according to multiple criteria.
Sun et al. BMC Bioinformatics 2012 13:331 doi:10.1186/1471-2105-13-331