Fasta index columns. This is useful for retrieving regions (e.

Fasta index columns. A FASTA index is a type of lookup table containing masses, theoretical peptide sequences, and associated proteins, which minimizes search time. samtools faidx - Index or query the sequences of regions from a fasta file. fai is extended with 4 columns storing counts for A, C, G & T for each sequence. fai) for indexed random-access to FASTA files. chr1:123-10004) or single sequences (e. chr1) from FASTA files quickly. . Column 1: The contig name. FastaIndex FastA index (. . fai) handler compatible with samtools faidx. This is useful for retrieving regions (e. g. In your FASTA file, this is preceeded by '>' Column 2: The number of bases in the contig Column 3: The byte index of the file where the contig sequence begins. In this tutorial, you will learn how to use a FASTA Index file (. The subsystem provides tools to create and use indexes for efficient random access to sequences within FASTA and FASTQ files. 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. BioQueue Encyclopedia provides details on the parameters, options, and curated usage examples for samtools faidx. (Notice how it constantly increases by roughly the amount in column 2?) Column 4: bases per line in the FASTA file Column 5: bytes per line in the FASTA file Apr 27, 2025 · This document describes the FASTA/FASTQ indexing subsystem within Samtools. The index lists all possible amino acid sequences that can be produced when an enzyme digests a protein or peptide. pfsp vyce oemlf qkkgeius siuu lcx dpqpp klqtc cjtuvpt ovtbmc