What does FASTA format look like?
A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (“>”) symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length.
What is Samtools Faidx?
This tool produces a . fai index file for FASTA files. The input file can be either uncompressed or in BGZF format, see . One of the options is to input a regions file with the regions to extract.
How do I create a FASTA file?
Use a text editor (for example, WordPad) to prepare the FASTA file of nucleotide sequences. Be sure to save your file as Plain Text or Text document. If you are not sure that the “Save” option in your program does this automatically, use “Save As…”. In the “Save as type:” pull-down menu, select “Text Document”
What is a genome index file?
analysis. sequence. index files. The sequence. index file contains a list of all the sequence data produced by the project, pointers to the file locations on the ftp site and also all the meta data associated with each sequencing run.
How FASTA format is written?
FASTA format: A sequence record in a FASTA format consists of a single-line description (sequence name), followed by line(s) of sequence data. The first character of the description line is a greater-than (“>”) symbol. Any non-alphabetical character in the input sequences is ignored by MUMMALS.
How do I read a Fasta file?
Sequence in FASTA format begins with a single-line description (distinguished by a greater-than ‘>’ symbol), followed by sequence data on the next lines. Lines starting by a semicolon ‘;’ are ignored, as in the original FASTA program (Pearson and Lipman 1988).
What is Fasta FAI file?
An fai index file is a text file consisting of lines each with five TAB-delimited columns for a FASTA file and six for FASTQ: NAME. Name of this reference sequence. LENGTH. Total length of this reference sequence, in bases.
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 is FASTA FAI?
The fasta. fai is the fasta index, and the one you posted looks legit. For each row: Column 1: The contig name. In your FASTA file, this is preceeded by ‘>’
What is FA FAI file?
What is Fasta index?
What is Fasta FAI?
What does an index file in FASTA mean?
The index file typically has the same filename as the corresponding FASTA/FASTQ file, with.fai appended. An fai index file is a text file consisting of lines each with five TAB-delimited columns for a FASTA file and six for FASTQ:
What does a FAI index file look like?
An fai index file is a text file consisting of lines each with five TAB-delimited columns for a FASTA file and six for FASTQ: The NAME and LENGTH columns contain the same data as would appear in the SN and LN fields of a SAM @SQ header for the same reference sequence.
How does faidx extract subsequences in FASTA format?
Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create .fai on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format. The input file can be compressed in the BGZF format.
How to create a.dict file from a FASTA file?
We use the CreateSequenceDictionary tool to create a .dict file from a FASTA file. Note that we only specify the input reference; the tool will name the output appropriately automatically. This produces a SAM-style header file named ref.dict describing the contents of our FASTA file.