Unfortunately there have been many variations of the original GFF format and many have since become incompatible with each other. The latest accepted format GFF3 has attempted to address many of the issues that were missing from previous versions. Skip to content. The official documentation for the GFF3 format can be found here General Feature Format GFF is a tab-delimited text file that holds information any and every feature that can be applied to a nucleic acid or protein sequence.
Pretty simple, right? The top line holds information pertaining to the sequence below. Without this informative first line, we just have a raw format. Here is a list of major database sequence identifers:. The line immediately proceeding the identifier is the raw sequence.
For more specific types, we can use the following:. This is a single file with several sequences, and is often used for multi-alignment programs like ClustalW or multialign.
The FASTA format is extremely simple with just two lines per sequence - the first is for the description, the other for the raw sequence. The simplicity is nice when running a quick pairwise alignment, but limiting when we need more information per sequence. With next-generation sequencing instruments pumping out millions of reads per run, scientists needed a way to check the quality of each base call. To document both the sequence and the probability of each of being correct, scientists came up with the FASTQ format.
The "Q" comes from quality, as in the quality of the read. In addition to storing biological sequence information, it also adds a line for the quality scores. The first line begins with an ' ' character and contains the sequence identifier with an optional description. The fourth line encodes the quality scores per each base call. This line must have the same length as the sequence in line 2. Scores range from! The p is the probability that the corresponding base call is incorrect, and Q is the Phred quality score which can range from 0 to SAMtools is a suite of utilities that allow for efficient post-processing of short DNA sequence read alignments.
The program includes several command line programs such as view , sort , and index that allow for next-generation sequence data processing. In addition to regular sequence reads, SAM includes alignment data that link short reads to a reference sequence. The SAM format is simple to parse, generate and check for errors.
Thus, researchers found a way to compress it into a binary format without losing the ability to manipulate it. BAM contains indexable representation of nucleotide sequence alignments, allowing for intensive data processing in production pipelines. BED is a tabs-delimited file format allows users to define how data lines of an annotation track are displayed. If you're unfamiliar with an annotation track, they're simply the lines that are displayed on a genome browser.
The number of columns must be consisted throughout each row of the file. BEDtools - Read the Docs. The Wiggle format. It is primarily used to store values such as GC percentage, probability scores and transcriptome data. Instead of specifying a value for each nucleotide position, wig allows you to bind values to entire regions that follow a certain pattern.
This allows for efficient data handling, as only parts of the file are extracted and processed when viewing particular regions on a genome browsers. For a conversion, use the WigToBigWig program. On the top of each block is the track declaration line , which defines the data elements with a number of options. There are several options we can place on the first line which characterizes that particular block of information. The variableStep option is the more common option.
It includes the chromosome position in one column, and data values in another. We may have the chromosome number and an optional parameter known as span , which tells us the number of bases each value should cover. For more information about this file format, see the documentation on the GMOD wiki. Search terms. Human Homo sapiens. Important note : the seq ID must be one used within Ensembl, i. See the example GFF output below.
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