Sentence examples for coordinates in bed from inspiring English sources

Files with peak coordinates in bed format were downloaded from the NCBI GEO depository [GEO GSE38379].

To analyze multiple loci, users may specify the input genomic coordinates in BED format, which is widely used in high-throughput genome analyses.

Patterns of conservation within a target sequence can be aggregated using the halLiftover tool, which maps coordinates in a BED file to an arbitrary target in the alignment.

The coordinates in the BED file provided by Nam and co-workers were lifted from the mm9 to mm10 mouse genome using the LiftOver tool from UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgLiftOver).

The isotherm is slightly favorable (i.e., concave downward) in order to justify the assumption that axial gradients of concentration are independent of the radial coordinate in the bed, as in the classical problem of Taylor diffusion.

Genomic coordinates of mature miRNAs were extracted (in BED format) from the annotation file in miRBase version 18.

For each gene, the genomic coordinates of exons, introns, 5/3′UTRs and extensions are stored in BED format and intersected with the mapping coordinates of the clusters.

The input for GimmeMotifs is a file in BED format containing genomic coordinates, e.g. peaks from a ChIP-seq experiment or a FASTA file.

cnvOffSeq also requires the coordinates of targeted coding regions (to be excluded) in BED format.

A genomic feature file was also built in BED format, which describes the coordinates of all annotated repetitive element instances.

Genomic coordinates of reads mapping to the genome without mismatch were obtained (in BED format) using a Python script from mapping results.