Sentence examples for map reads to from inspiring English sources

To map reads to splice junctions, TopHat first enumerates all canonical donor and acceptor sites within the island sequences (as well as their reverse complements).

To map reads to the reference, we used a combination of Mosaik (a BLAT-like tool optimized for aligning short-read sequencing reads to a reference; ) and BLAST [ 21], which allowed us to map between 71.3% and 83.7% of the reads that passed our filters, representing 1.2 to 1.9 million reads.

These experiments were done in replicates of two and the replicate data were analyzed using TopHat v1.4.1 and Cuffdiff v1.3.048 to map reads to a reference mouse genome assembly (mm9) and expression differences against the Ensembl release 67 gene model were determined.

The spliced read mapper TopHat version 1.4.1 (Trapnell et al. 2012) was used to map reads to rice O. sativa Nipponbare genome (MSU release 6.16).

Illumina whole-genome shotgun 100-bp paired-end DNA sequencing data were filtered to obtain high-quality sequence data and to map reads to the Nipponbare reference genome sequence, which as downloaded from NCBI.

While this may be an under-estimation of the error rate due to our inability to map reads to all nucleotides in the assembled rice genome and the lack of the requisite read depth at every nucleotide, we were able to assess 321 of the 373 Mb assembly for errors.

Hence, neither Bowtie nor MAQ should be used for mapping reads to quantify gene expression.

Gene expression profiling was measured by mapping reads to assembled sequences using SOAP [66].

One further limitation of Bowtie and MAQ is the random assignment of equally well mapped reads to the corresponding genes.

Tools for analyzing RNA-Seq data include TopHat [7], which analyzes mapped reads to identify splice junctions between exons.

We therefore assembled the mapped reads to obtain 19,752 NTRs.