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samtools sort -m 5000000 unsorted_in.bam sorted_out Read the specified unsorted_in.bam as input, sort it in blocks up to 5 million k (5 Gb) [ units verification needed ] and write output to a series of bam files named sorted_out.0000.bam , sorted_out.0001.bam , etc., where all bam 0 reads come before any bam 1 read, etc. [ verification needed ]
BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4] The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them.
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]
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression. MultiDE; Myrna is a pipeline tool that runs in a cloud environment (Elastic MapReduce) or in a unique computer for estimating differential gene expression in RNA-Seq datasets. Bowtie is employed for short read ...
Selective access to a CRAM file is granted via the index (with file-name suffix ".crai"). On chromosome and position sorted data this indicates which region is covered by each slice. On unsorted data the index may be used to simply fetch the N th container. Selective decoding may also be achieved using the Compression Header to skip specified ...
The Z-ordering can be used to efficiently build a quadtree (2D) or octree (3D) for a set of points. [4] [5] The basic idea is to sort the input set according to Z-order.Once sorted, the points can either be stored in a binary search tree and used directly, which is called a linear quadtree, [6] or they can be used to build a pointer based quadtree.
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.