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Results for "Samtools"

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• • Jit@jit.aber

  

  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

  2858 days ago

• • Jit@jit.aber

  

  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

  2851 days ago

• • Shruti Paniwala@shruti

  

  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

  2733 days ago

• • Jit@jit.aber

  

  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

  2593 days ago

• • Aaryan Lokwani@aaryan

  

  Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools

  Tags: Fasta, Index, Length, Count, Size, Samtools

  2129 days ago

• • Poonam Mahapatra@poonam

  

  #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

  2857 days ago

• • Radha Agarkar@radhaagarkar

  

  Unable to index fasta file with samtools !

  I am unable to index fasta file with samtools ! It return "different line length in sequence" error message . How to fix it?  nc@radha[Downloads] samtools faidx dedup.genome.scf.fasta_assembly.fna [][fai_build_core] different line length in sequence 'jcf7180000001219'.Could not build fai in...

  Tags: samtools, faidx, index, length, sequence

  2236 days ago

• • Rahul Nayak@rahul

  

  Error: Could not find dictionary next to reference file file

  htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa

  Tags: dictionary, next, reference, file, samtools, SAMException

  1529 days ago

• • biogeek@biogeek

  

  error: mate does not occur next to it in your BAM file. How to fix it ?

  *****WARNING: Query v300043428L4C001R0481272249 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.

  Tags: samtools, paired, pe, error, mates reads

  1449 days ago

• • LEGE@lege

  

  How to resolve samtools index error "Chromosome blocks not continuous" ?

  samtools index mappedPairs.sorted.bam return the following error ... [bam_sort_core] merging from 0 files and 2 in-memory blocks...[E::hts_idx_push] Chromosome blocks not continuoussamtools index: failed to create index for "mappedPairs.sorted.bam"

  Tags: samtools, index, sort, bam, reads

  982 days ago