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The view command filters SAM or BAM formatted data. Using options and arguments it understands what data to select (possibly all of it) and passes only that data through. Input is usually a sam or bam file specified as an argument, but could be sam or bam data piped from any other command.
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [ 2 ] [ 3 ] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments ...
^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality $ (dollar) marks the end of a read segment * (asterisk) is a placeholder for a deleted base in a multiple basepair deletion that was mentioned in a previous line by the - [0-9] + [ACGTNacgtn] + notation
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
In computing, fc (File Compare) is a command-line program in DOS, IBM OS/2 and Microsoft Windows operating systems, that compares multiple files and outputs the differences between them. [2] [3] It is similar to the Unix commands comm, cmp and diff.
A workflow can be run using the graphical interface or launched from the command line. The graphical interface also allows controlling the workflow execution, storing the parameters, and so on. There is an embedded library of workflow samples to convert, filter, and annotate data, with several pipelines to analyze NGS data developed in ...
COMP.COM (among other commands) in IBM PC DOS 1.0.. In DOS, the comp command first appeared in PC DOS 1.0 [7] and has been included in most versions of MS-DOS and PC DOS.A newer command, fc was added in DOS 3.3 which allows for line comparisons in addition to binary comparisons.
It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. SpliceR An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.