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Results for "bam"

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• • Jit@jit.aber

  

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

  Tags: BAM, SAM, R, NGS, Plot

  2831 days ago

• • Shruti Paniwala@shruti

  

  Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM

  Tags: R, Plot, Genome, Image, NGS, BAM

  2732 days ago

• • Jit@jit.aber

  

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

  Tags: SAM, BAM, File, Explain

  2610 days ago

• • Jit@jit.aber

  

  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

  2610 days ago

• • Jit@jit.aber

  

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

  Tags: SAM, BAM

  2605 days ago

• • Jit@jit.aber

  

  Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

  Tags: SAM, BAM, Convert, Tab

  2604 days ago

• • Jit@jit.aber

  

  Alfred: BAM Statistics and Feature Counting

  The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfred dependencies are included as submodules so you need to do a recursive clone. git clone --recursive https://github.com/tobiasra...

  Tags: Alfred, BAM, Statistics, Feature, Counting

  2277 days ago

• • Jit@jit.aber

  

  Bioinformatics tutorial https://jasonjwilliamsny.github.io/wrangling-genomics/01-automating_a_workflow.html #Workflow #Tutorial #BAM #SAM #SNP

  Tags: Workflow, Tutorial, BAM, SAM, SNP

  2191 days ago

• • Jit@jit.aber

  

  pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

  pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver optio...

  Tags: pbalign, maps, PacBio, reads, reference, sequences, alignments, BAM, NGS

  2156 days ago

• • Neelam Jha@neelam

  

  Generate consensus from BAM file samtools mpileup -uf chr5B_leaf_rust.fasta M27454_5B_reads_sorted.bam | bcftools call -c | vcfutils.pl vcf2fq #BAM #Consensus

  Tags: BAM, Consensus

  2015 days ago

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