Sentence examples for using the bowtie alignment from inspiring English sources

To accomplish this, we first align the reads to the transcript sequences using the Bowtie alignment tool (Langmead et al., 2009), preserving possible multiple alignments to different transcripts.

To gain an overview of small RNA distribution in the genome, we mapped small RNAs using the Bowtie alignment tool [ 23].

In order to find repeat-associated siRNA in maize sRNA libraries, we aligned the siRNA candidates (Table  1) in the maize repeat database (Repbase, v.18) using the Bowtie alignment and allowing three mismatches.

We incrementally divided each gene into k-mers (of between 15 and 1,000 nucleotides) and used the Bowtie alignment algorithm [ 12] to report every instance of a k-mer from one gene that perfectly matched the sequence of another gene.

We used the Bowtie alignment tool [ 23] to filter out reads that mapped to structural RNAs: tRNA (1,640 reads), rRNA (3,456 reads) and repetitive elements (EhSINEs, EhLINEs and EhERE elements) (8,073 reads).

Sequence alignment was performed using the BOWTIE aligner (Langmead et al. 2009), modified for color space reads.

TopHat internally uses the Bowtie aligner.

The Illumina Human Bodymap 2.0 RNA-seq data (GSE30611) was downloaded from GEO and mapped to NCBI's transcript reference using the Bowtie and Tophat alignment algorithms with default parameters (Langmead et al., 2009; Trapnell et al., 2009).

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.

ChimeraScan 0.4.5a default parameters were used, including using the bowtie -best -strata option for alignment, 2 mismatches tolerated at breakpoints, 4 bp minimum overlap required to call spanning reads, 8 bp anchor region where mismatch checks are enforced, and 0 mismatches allowed within the anchor region.

In both cases, we limited the alignments to at most 3 mismatches using the Bowtie '–v 3' setting.