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The STAR program with default parameters was used to map the sequenced reads to the reference genome and to find those that spanned exon exon junctions.
The next step is to map the sequenced DNA to the genome using a DNA alignment algorithm.
SNP calling procedures map the sequenced genome to a reference and examine positions of variation from the reference.
Since we used the full genome's sequence to map the sequenced reads the formal possibility remains that perhaps a significant portion of the orphan reads originate from the exon-exon junctions of spliced protein-coding transcripts.
Typically, failure to detect genetic variants in NGS data is a result of the inability of the alignment software to map the sequenced variant reads to the genomic region, or a failure to sample the variant allele sufficiently or at all [ 1].
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Eland_extended algorithm was used to map the sequences to human genome (hg18).
To integrate this genetic map with the BAC-based physical map, the sequences of genetic markers were aligned with BES from the physical map using BLAST.
Longitudinal investigations using structural magnetic resonance imaging (MRI) provide a framework to map the sequence of neuroanatomical changes at all levels of this model.
The second approach attempts to map the sequence reads to a position within a reference genome.
BLAT was used to map the sequences to the reference genome.
In this study, we map the sequence reads to pre-miRNAs rather than the mature miRNAs.
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