What is a genome file Bedtools?

What is a genome file Bedtools?

Genome file format When using the UCSC Genome Browser, Ensemble, or Galaxy, you typically indicate which which species/genome build you are working. The way you do this for bedtools is to create a “genome” file, which simply lists the names of the chromosomes (or scaffolds, etc.) and their size (in basepairs).

What is Bedtools?

The BEDTools allow a fast and flexible way of comparing large datasets of genomic features. The BEDtools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

What is Bedpe format?

BEDPE File Format A file format based on the BED format to concisely describe disjoint genome features, such as structural variations or paired-end sequence alignments.

What is BED file in bioinformatics?

The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. As a result of this increasingly wide use, this format has become a de facto standard in bioinformatics without receiving any official specifications.

What does Bedtools intersect do?

bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both BED/GFF/VCF and BAM files as input.

How does Bedtools coverage work?

The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.

What language is Bedtools?

C++
The software is written in C++ and supports alignments in BAM format (Li et al., 2009) through use of the BAMTools libraries (Barnett et al., http://sourceforge.net/projects/bamtools/).

How do you convert BAM to BED?

For example:

1. Convert BAM alignments to BED format. Code: $ bamToBed -i reads.bam > reads.bed.
2. Convert BAM alignments to BED format using edit distance (NM) as the BED “score”. Default is mapping quality. Code: $ bamToBed -i reads.bam -ed > reads.bed.
3. Convert BAM alignments to BEDPE format.

What is a bigWig file?

The bigWig format is for display of dense, continuous data that will be displayed as a graph. BigWig files are created initially from WIG type files, using the UCSC program wigToBigWig. Alternatively, bigWig files can be created from bedGraph files, using the UCSC program bedGraphToBigWig.

What is WIG file?

WIG File Format – Definition and supported options. The WIG (wiggle) format is designed for display of dense continuous data such as probability scores. Wiggle data elements must be equally sized; if you need to display continuous data that is sparse or contains elements of varying size, use the BedGraph format instead …