How do I convert a BAM file to bed?

For example:

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 is BAM format?

A BAM file (*. bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb. Header—Contains information about the entire file, such as sample name, sample length, and alignment method. …

What does Samtools view do?

The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.

What is a Bedpe file?

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

How do I view a BAM file?

BAM files can be opened from remote locations (ftp, http) and from local computers. For viewing BAM files, an index file must be found in the same directory as the BAM file. The index should be named by appending “. bai” to the BAM file name.

How do I get a UCSC bed file?

Download a bed file for all UCSC exons using UCSC Table Browser:

track: UCSC Genes.
table: knownGene.
output format: BED – browser extensible data.
press get output.
select option Exons.
press get BED.

Are BAM files normalized?

bamCoverage offers normalization by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM), counts per million (CPM), bins per million mapped reads (BPM) and 1x depth (reads per genome coverage, RPGC).

How to convert BAM files to bed files?

Moreover, to generate R data structures containing reads information, the function bedtolist must be run on the resulting BED files. For these reasons the authors suggest the use of bamtolist . Character string specifying the path to the folder storing BAM files.

How to write uncompressed Bam output in bedtobam?

Write uncompressed BAM output. The default is write compressed BAM output. Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format. In this case, bedToBam will convert blocked BED features (e.g., gene annotations) into “spliced” BAM alignments by creating an appropriate CIGAR string.

How to write Bam alignments in bed format?

bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. Write BAM alignments in BEDPE format. Only one alignment from paired-end reads will be reported.

What is the name of the bed in Bam?

By default, each alignment in the BAM file is converted to a 6 column BED. The BED “name” field is comprised of the RNAME field in the BAM alignment. If mate information is available, the mate (e.g., “/1” or “/2”) field will be appended to the name.