Sentence examples for using the bowtie program from inspiring English sources
All unique tags (including those with a single count) were mapped to the NCBI Mouse Assembly Build 37.1 using the Bowtie program [ 74].
After cleaning the data, we mapped them on the human genome reference sequence version hg19 using a mapping tool of Avadis NGS (Agilent Technologies, Santa Clara, CA, USA) or using the Bowtie program.
For digital gene expression analysis, the raw digital gene expression counts were measured by quantifying the number of Illumina GA-II reads that were mapped to the reference sequences (MSGI 1.0 or Mt3.0 cds) using the bowtie program [ 47].
As an initial step to evaluate the utility of MSGI 1.0 and Mt3.0 cds as reference sequences for transcript profiling of alfalfa, the Illumina EST reads generated in this study were mapped to MSGI 1.0 and Mt3.0 cds sequences using the bowtie program [ 47] (see Methods for details).
All the Illumina reads that were allocated to such contigs were obtained using the Bowtie 2 program version 2.1.0.
Reads were aligned to the EBV-2 RefSeq genome (NC_009334.1) using the Bowtie 2 program [ 128] (data given in Additional file 5).
First, the quality-trimmed sequencing reads of the library were mapped to the assembled transcriptome using the Bowtie assembler program [ 48].
Authenticity of the assembled genomic sequences described above was examined by aligning the sequences of subcontigs contained in the scaffolds of the genomic assemblies with the contig sequences of the BAC clones using the Bowtie 2 program.
Mapping runs were conducted using the Bowtie v0.12.7 algorithm and program [ 53]. "Unique" means that a read is only included in the mapping results file if it maps to only one unique location in the reference.
All reads were realigned to the NCBI m37 version of the mouse genome assembly using the Bowtie [26] short read alignment program considering the 22 chromosome assemblies.
Sequences of the form N20-NGG in the assigned region were first extracted using the Bowtie software (version 0.12.8).
