Table of Contents
What is a bedGraph?
BedGraph is a file format that allows display of continuous-valued data in a track in genome browsers that support the format. At present, JBrowse does not support bedGraph, so we cannot use data in this format for PomBase. If you have data in bedGraph format, we recommend converting to WIG or bigWig format.
What is wiggle format?
The wiggle (WIG) format is an older format for display of dense, continuous data such as GC percent, probability scores, and transcriptome data. Wiggle data elements must be equally sized. The bedGraph format is also an older format used to display sparse data or data that contains elements of varying size.
What are Fastq and BAM?
FASTQ: a text-based format for storing nucleotide sequences (reads) and their quality scores. [1] BAM: The Sequence Alignment/Mapping (SAM) format is a text-based format for storing read alignments against reference sequences and it is interconvertible with the binary BAM format. [2]
How do I install Bedtools on Mac?
Instructions
- To install bedtools, run the following command in macOS terminal (Applications->Utilities->Terminal) sudo port install bedtools Copy.
- To see what files were installed by bedtools, run: port contents bedtools Copy.
- To later upgrade bedtools, run: sudo port selfupdate && sudo port upgrade bedtools Copy.
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).
What is FASTA vs FASTQ?
FASTA (officially) just stores the name of a sequence and the sequence, unofficially people also add comment fields after the name of the sequence. FASTQ was invented to store both sequence and associated quality values (e.g. from sequencing instruments).
What do you use Bedtools for?
The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
When should you use a BED file?
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.
What should a BED file look like?
BED format is a simple way to define basic sequence features to a sequence. It consists of one line per feature, each containing 3-12 columns of data, plus optional track definition lines. These are generally used for user defined sequence features as well as graphical represntations of features.