Results for "samtools"

Tags

  • 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

    2828 days ago

  • 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

    2710 days ago

  • 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

    2106 days ago

  • #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

    2834 days ago