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Results for "BAM"

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• • Abhimanyu Singh@abhimanyu

  

  #Intersect your bed data with coverage $ bedtools genomecov -ibam aln.bam -bga | awk '$4==0' | bedtools intersect -a cds.bed -b - -f 1.0

  1991 days ago

• • Jit@jit.aber

  

  Ribbon genomics http://genomeribbon.com/ #Visualization #Ribbon #Graph #Genome #BAM #SAM #Mummer

  1978 days ago

• • Jit@jit.aber

  

  #Split the #BAM file $ /home/urbe/Tools/bamtools/bin/bamtools split -in improved3.fasta.sorted.bam -reference #bamtools

  1957 days ago

• • Neelam Jha@neelam

  

  (smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta

  1918 days ago

• • Jit@jit.aber

  

  samtools mpileup -uf reference.nt mapping.bam | bcftools call -c | vcfutils.pl vcf2fq > consensus.fasta #Genome #Assembly #Reference

  1910 days ago

• • Jit@jit.aber

  

  samtools view -Sb pilonCor_round1.fasta.out.sam | samtools sort -m 4G -@ 40 -o pilonCor_round1.fasta.out.sorted.bam - && samtools index -@ 40 pilonCor_round1.fasta.out.sorted.bam #SAM2BAM

  1909 days ago

• • Jit@jit.aber

  

  Get the secondary hists reads count from SAM awk '{ print $2 }' out.sam| grep "2048" | wc -l #SAM #BAM #Secondary #Hits

  1830 days ago

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