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Results for "Samtools"

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• • Jit@jit.aber

  

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

  2621 days ago

• • Jit@jit.aber

  

  samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam

  2294 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

  2032 days ago

• • Jit@jit.aber

  

  Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences

  1965 days ago

• • Jit@jit.aber

  

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

  1916 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

  1915 days ago

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