Search results
Results from the WOW.Com Content Network
samtools view -bS sample.sam > sample.bam. Convert a sam file into a bam file. The -b option compresses or leaves compressed input data. samtools view sample_sorted.bam "chr1:10-13" Extract all the reads aligned to the range specified, which are those that are aligned to the reference element named chr1 and cover its 10th, 11th, 12th or 13th ...
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 ...
bam-lorenz-coverage A tool that can generate Lorenz plots and Coverage plots, or export these statistics to text files, directly from BAM file(s). [ 7 ] dupRadar [ 8 ] An R package which provides functions for plotting and analyzing the duplication rates dependent on the expression levels.
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 ...
It is developed in Java and open source. Both: Albrecht F: 2015 HMMER: Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST: Both: Durbin R, Eddy SR, Krogh A, Mitchison G [6] 1998 HH-suite: Pairwise comparison of profile Hidden Markov models; very sensitive: Protein: Söding J [7] [8] 2005/2012 IDF Inverse ...
Change any of the following settings, then click Save to finalize your selection: • Inbox Style Select what type of inbox you want. • Mail Away Message Create and enable away messages.
Without a clear schema for read names, their function remains that of a unique read id, conveying the same amount of information as a read serial number. See various SRA Toolkit issues for details and discussions. Also note that fastq-dump converts this FASTQ data from the original Solexa/Illumina encoding to the Sanger standard (see encodings ...
BEDTools: program allowing the manipulation of coordinate sets and the extraction of sequences from a BED file. [6] BEDOPS: a suite of tools for fast boolean operations on BED files. [8] BedTk: a faster alternative to BEDTools for a limited and specialized sub-set of operations. [9] covtobed: a tool to convert a BAM file into a BED coverage ...