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samtools view -h -b sample_sorted.bam "chr1:10-13" > tiny_sorted.bam. Extract the same reads as above, but instead of displaying them, writes them to a new bam file, tiny_sorted.bam. The -b option makes the output compressed and the -h option causes the SAM headers to be output also.
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 ...
The browser allows users to visualize and browse large (up to hundreds of millions of short reads) next generation sequence assemblies. It supports SAM, [20] BAM (the binary version of SAM), and ACE formats. Before browsing assembly data in UGENE, an input file is converted to a UGENE database file automatically. This approach has its pros and ...
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.
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BamView BamView is a free interactive display of read alignments in BAM data files. It has been developed by the Pathogen Group at the Sanger Institute. BrowserGenome: [144] web-based RNA-seq data analysis and visualization.
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Compressed Reference-oriented Alignment Map (CRAM) is a compressed columnar file format for storing biological sequences aligned to a reference sequence, initially devised by Markus Hsi-Yang Fritz et al. [1] CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file ...