What are bed files used for?
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project and then adopted by other sequencing projects.
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.
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.
How do you make a genome file?
- To make a genome file (for bed tools) using reference genome.
- 1) Use samtools to generate fasta index samtools faidx lyrata_genome.fa – this will create a lyrata_genome.fa.fai (index file)
- 2) take the index file, then use awk.
- if space desired between columns do this.
What are BAM files?
A BAM file (. bam) is the binary version of a SAM file. A SAM file (. sam) is a tab-delimited text file that contains sequence alignment data. These formats are described on the SAM Tools web site: http://samtools.github.io/hts-specs/.
How do I view a BED file?
Programs that open BED files
- Integrated Genome Browser. Any text editor.
- Integrated Genome Browser.
- Linux. Integrated Genome Browser.
- Web. UCSC Genome Browser.
How do I view a .BED file?
How do you convert BAM to BED?
- Convert BAM alignments to BED format. Code: $ bamToBed -i reads.bam > reads.bed.
- 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.
- Convert BAM alignments to BEDPE format.
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.
What does Bedtools merge do?
bedtools merge combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
What is the default output format of genomecoveragebed?
By default, genomeCoverageBed will compute a histogram of coverage for the genome file provided. The default output format is as follows: 1. chromosome (or entire genome) 2. depth of coverage from features in input file 3. number of bases on chromosome (or genome) with depth equal to column 2.
What does the-max option do in BedTools genomecov?
fraction of bases on chromosome (or entire genome) with depth equal to column 2. Using the -max option, bedtools genomecov will “lump” all positions in the genome having feature coverage greater than or equal to -max into the -max histogram bin.
How to quickly identify regions of the genome with sufficient coverage?
Using this format, one can quickly identify regions of the genome with sufficient coverage (in this case, 10 or more reads) by piping the output to an awk filter. The -bg option reports coverage in BEDGRAPH format only for those regions of the genome that actually have coverage.
How do you normalize coverage in a histogram?
Combine all positions with a depth >= max into a single bin in the histogram. Scale the coverage by a constant factor. Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). Default is 1.0; i.e., unscaled.