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sort samtools sort -o sorted_out unsorted_in.bam. Read the specified unsorted_in.bam as input, sort it by aligned read position, and write it out to sorted_out. Type of output can be either sam, bam, or cram, and will be determined automatically by sorted_out's file-extension. samtools sort -m 5000000 unsorted_in.bam sorted_out
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. [4]
The SAM format consists of a header and an alignment section. [1] 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 ...
Import of data is possible from FastQ files, BAM or SAM format. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Results are presented in HTML permanent reports. FastQC can be run as a stand-alone application or it can be integrated into a larger pipeline solution.
The SAM/BAM files use the CIGAR (Compact Idiosyncratic Gapped Alignment Report) string format to represent an alignment of a sequence to a reference by encoding a sequence of events (e.g. match/mismatch, insertions, deletions).
CRAM was designed to be an efficient reference-based alternative to the Sequence Alignment Map (SAM) and Binary Alignment Map (BAM) file formats. It optionally uses a genomic reference to describe differences between the aligned sequence fragments and the reference sequence, reducing storage costs.
Signed binary angle measurement. Black is traditional degrees representation, green is a BAM as a decimal number and red is hexadecimal 32-bit BAM. In this figure the 32-bit binary integers are interpreted as signed binary fixed-point values with scaling factor 2 −31, representing fractions between −1.0 (inclusive) and +1.0 (exclusive).
Variant calling in RNA-Seq is similar to DNA variant calling and often employs the same tools (including SAMtools mpileup [134] and GATK HaplotypeCaller [135]) with adjustments to account for splicing.