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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 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.
Name Creates [a] Modifies? [b]Mounts? [c]Writes/ Burns? [d]Extracts? [e]Input format [f] Output format [g] OS License; 7-Zip: Yes: No: No: No: Yes: CramFS, DMG, FAT ...
No, but can read-show 2D structure annotations ClustalW No Dotplot, 6 frame translation, Blast Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS Proprietary, freeware: No Cross-platform -Mac OS, Linux, Windows Official website: CLC viewer (free version) Commercial version only Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various UPGMA, NJ
^ (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 self-extracting executable may need to be renamed to contain a file extension associated with the corresponding packer; archive file formats known to support this include ARJ [1] and ZIP. [2] [3] Typically, self-extracting files for Microsoft operating systems such as DOS and Windows have a .exe extension, just like any other executable file.
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 ...