Sentence examples for map reads that from inspiring English sources

It is therefore able to map reads that span introns without requiring prior transcript annotations or for the detection of large deletions in genomic data.

Indeed, strand-specificity information is useful to correctly map reads that do not contain polyA tails or splice junctions and represent a challenge in the annotation step of RNA-seq reads.

These reads are much more difficult to map than reads that match the reference exactly, and because of this, existing tools generally only map reads that have ≤3 mismatches relative to the reference genome.

Accordingly, recent programs, such as Bowtie (Langmead et al., 2009), BWA (Li and Durbin, 2009) and SOAP2 (Li et al., 2009), have shown how suffix arrays (Manber and Myers, 1993), compressed using a Burrows–Wheeler Transform (BWT; Burrows and Wheeler, 1994), can rapidly map reads that are exact matches or have a few mismatches or short insertions or deletions (indels) relative to the reference.

Additional coping strategies involve using multiple read mappers or more computationally intense software such as Blast to improve mapping results since they can be used to map reads that are unmapped by less computationally intense software such as Bismark and Bowtie2.

The uniquely mapped reads that mapped to a single location in the genome were analyzed for differential gene expression between the control and treatment samples using the R package DESeq v1.7.10 [ 61].

The expression level for each known and unannotated transcript was calculated as RPKM (Reads Per Kilobase exon Model per Million mapped reads) based on the number of uniquely mapped reads that completely overlap with the exonic regions.

SeaSight offers an import filter for mapped reads that can parse any tabular file as long as the essential information is present.

To test this, we re-mapped reads that match multiple genomic loci (group R) to the regions of low-coverage, this time randomly assigning ambiguously mapping reads to one of their genomic matches.

Precision is the fraction of mapped reads that are correctly mapped and recall is the fraction of correctly mapped reads that are retrieved.

Meanwhile, we filtered out the ambiguously mapped reads that have non-primary alignments and repetitive hits.