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Secondly, we realigned all the transcripts onto the reference genome.
The ENCODE authors used a probability based alignment tool to map RNA transcripts onto DNA.
Mapping of transcripts onto the A. gambiae genome was beneficial in the gene discovery process.
Let us now examine the manner in which ENCODE mapped RNA transcripts onto the genome.
Assembly quality was assessed by aligning the transcripts onto the scaffolds, and 97.5% mapping rate was observed (Additional file 1: Table S2).
The ASD pipeline does not cluster transcripts to assemble full-length transcripts; the pipeline maps transcripts onto 'known' genes from Ensembl [ 51] and delineate the unique splice patterns.
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One such mechanism is "leaky scanning" where a proportion of the scanning complexes bypass the uORF AUG and continue scanning the transcript onto a downstream start codon.
The expression level of all unique transcripts mapped onto the genome were quantified as reads per kilobase of exon model per million mapped (RPKM) values (Mortazavi et al. 2008).
In this group, 131 transcripts map onto human genomic regions with no annotation.
Almost one-fifth of the transcripts mapped onto non-coding genomic loci, and of which half showed no sequence similarity to annotated genes of the protist.
Expression levels of all unique transcripts mapped onto the full-length cDNAs and contigs were quantified using the RPKM values [ 61].
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