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Results for "SAM"

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• • 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

  1914 days ago

• • Abhimanyu Singh@abhimanyu

  

  https://broadinstitute.github.io/picard/explain-flags.html What does the SAM flags means #SAM #Flag

  1840 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

  1836 days ago

• • LEGE@lege

  

  #Estimate the #insert #size with mapped reads $ head -10000 mappings.sam | awk '{ if ($9 > 0) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print "n="N", mean="M", stdev="sqrt ((S2-M*M*N)/(N-1))}'

  1622 days ago

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