Results for "sam"

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  • List of popular bioinformatics software/tools

    In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.

    Tags: Bioinformatics, SamTool, SAM, BAM, IGV, BLAT, Software, Tools

    1679 days ago

  • Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS

    Tags: Extract, Ids, SAM, BAM, NGS

    1368 days ago

  • Picard

    Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Note that the information on this pag...

    Tags: Bioinformatics, NGS, Assembly, BAM, SAM, CRAM, Picard, FastQC, Tool, Software

    661 days ago

  • SAM flags

    Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag value, just enter the number in the field below. The...

    Tags: Bioinformatics, SAM, Flags, NGS

    600 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

    599 days ago

  • Fancy Oneliner for Bioinformatics !!

    This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder struct...

    Tags: Bioinformatics, Analysis, Visualization, SAM, BAM, Oneliner, NGS, metagenomics

    592 days ago

  • Plot the coverage in R http://cnr.lwlss.net/SeqCoverage/ #BAM #SAM #R #NGS #Plot

    Tags: BAM, SAM, R, NGS, Plot

    581 days ago

  • Understanding and manipulating SAM/BAM alignment files http://homer.salk.edu/homer/basicTutorial/samfiles.html #SAM #BAM #File #Explain

    Tags: SAM, BAM, File, Explain

    360 days ago

  • bedtools

    Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count,&...

    Tags: Bioinformatics, Analysis, Assembly, Genome, bedtools, View, Alignment, BAM, SAM

    360 days ago

  • SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm # Perl #SAM #BAM

    Tags: SAM, BAM

    355 days ago