Sentence examples for using the bowtie package from inspiring English sources

All non-annotated reads with a length of 16 30 nt were mapped to the hexaploid wheat genome (http://www.cerealsdb.uk.net/CerealsDB/Documents/DOC_CerealsDB.php) using the Bowtie package (version one), only perfectly matched sRNAs were used for further analysis.

Sequences of the form N20-NGG in the assigned region were first extracted using the Bowtie software (version 0.12.8).

bogorensis genomic DNA sequence and processed using the Bowtie and SAMtools software package.

Sequencing reads from all 12 transcriptome libraries were first pooled and mapped to the Eucalyptus genome sequence scaffolds using the Bowtie [ 45] and TopHat [ 46] software packages.

This maps the reads back to the assembled transcripts using the bowtie aligner.

TopHat internally uses the Bowtie aligner.

These reads were mapped to the reference genome using the software package Bowtie allowing up to one mismatch and forcing uniqueness [ 12].

Reads that could not be mapped initially by Tophat were examined for evidence of polyA tails, trimmed to contain non-polyA sequences, and mapped to the reference genome using the software package Bowtie [ 12].

Remaining reads were mapped to the T. brucei genome using Bowtie [56] and aggregated into transcript regions using the Genominator package [57].

For each of the six Illumina samples, reads were mapped onto the Trinity/Illumina assembly using Bowtie 2 [ 51], and transcript abundance for each sample was estimated using the RSEM package [ 52].

Quality filtered RNA-seq reads were analyzed using the "Tuxedo Suite" software packages [ 46]: Bowtie [ 47] v0.12.7, Tophat [ 48] v1.3.2, Cufflinks [ 49] v1.1.0 and a reference genome of potato [ 9].