Results for "Samtools"

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  • Samtools Primer !!

    SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions    1.0: May 30, 2013: First public release on biobits.org.    1.1: July 24, 2013: Updated wi...

    Tags: Bioinformatics, NGS, Sequence, Samtools, Primer, Tutorial

    456 days ago

  • Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

    Tags: SAM, BAM, Samtools, Tricks, NGS

    449 days ago

  • Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

    Tags: Samtools, Fasta, Extract, Multifasta

    331 days ago

  • HTSlib

    Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel ...

    Tags: Bioinformatics, HTSlib, NGS, Samtools, C, Lib

    191 days ago

  • #Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

    Tags: Extract, Reads, BAM, region, samtools

    455 days ago

  • Samtools fields explained !

    From the SAM format specification, the fields are: Column Field Type Regexp/Range Brief description 1 QNAME String [!-?A-~]{1,255} Query template NAME 2 FLAG Int [0,216-1] bitwise FLAG 3 RNAME String \*|[!-()+-<>-~][!-~]* Reference sequence NAME 4...

    Tags: samtools, flags, fields, NGS, assembly, reads

    32 days ago