Sentence examples for initially aligned to from inspiring English sources

Raw reads were initially aligned to the full genome using an alignment score of 260 or greater, which for this dataset allowed for only one SNV per read.

For cases in which pyrosequencing was performed, reads were initially aligned to an HXB2 reference sequence using Mosaik [32].

For targeted sequence assemblies, the 1000 Genomes Project Consortium [14] employed TIGRA (L. Chen, unpublished: http://genome.wustl.edu/software/tigra_sv) to reassemble NGS reads that had been initially aligned to a reference.

This includes a two-step procedure, where all reads are initially aligned to the reference genome with Bowtie.

In brief, the reconstructed fractional anisotropy [ 16, 17] of each individual was initially aligned to the MNI template.

Particles were initially aligned to the total sum of 10 20 vertically oriented particles using SPIDER (Frank et al., 1996).

In addition, the amino acid sequences of MAPKs from four plants (Arabidopsis, O. sativa, G. max and G. raimondii) were initially aligned and used to construct phylogenetic trees.

Since we initially aligned RNA-seq reads to the maternal genome, we first check if the candidate indel RNA-DNA differences result from genuine maternal-paternal genome differences by realigning all the reads that can be mapped to the putative indel sites (including reads that support editing and reads that support the maternal genome version) to the paternal genome using BFAST.

Because the RNA-seq reads obtained above originate from human (the Toxoplasma parasite used in this experiment was grown on human foreskin fibroblast), mouse and Toxoplasma genes, we initially aligned all the reads to mouse (mm9) and human (hg18) genomes using Bowtie (v0.12.7) and Tophat (v2.0.0) with the default settings.

More detailed information of used taxa and sequences in each alignment data are summarized in the Additional file 7. To make these alignments, we initially aligned each gene portion by using MUSCLE [ 17] implemented in SeaView ver. 3.2 [ 18].

Initially, all 9,475,890 reads were aligned to a reference sequence of human genomic DNA, followed by quality trimming to remove low-quality reads and excluding reads with similarities to ambiguous human sequences, resulting in 9,309,538 reads (98.24%) with a possible human source (Fig. 1B).