Results for "BAM"

Tags

  • Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS

    Tags: Extract, Ids, SAM, BAM, NGS

    3598 days ago

  • #BAM file to fasta #conversion with #Samtool: samtools view filename.bam | \ awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

    Tags: BAM, conversion, Samtool

    2928 days ago

  • #BAM file to #fastaq #conversion with #Samtool: samtools view filename.bam | awk '{OFS="\t"; print "@"$1"\n"$10"\n+\n"$11}' >| filename.fastq

    Tags: BAM, fastaq, conversion, Samtool

    2928 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

    2835 days ago

  • #Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls

    Tags: Extract, tabbed, BAM

    2836 days ago

  • Check if BAM file is sorted or not use: for F in `find . -name "*.bam"`; do echo $F; samtools index ${F} ; done #Sort #BAM #Trick

    Tags: Sort, BAM, Trick

    2832 days ago

  • 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

    2829 days ago

  • Plot the coverage in R http://cnr.lwlss.net/SeqCoverage/ #BAM #SAM #R #NGS #Plot

    Tags: BAM, SAM, R, NGS, Plot

    2811 days ago

  • Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM

    Tags: R, Plot, Genome, Image, NGS, BAM

    2712 days ago

  • Understanding and manipulating SAM/BAM alignment files http://homer.salk.edu/homer/basicTutorial/samfiles.html #SAM #BAM #File #Explain

    Tags: SAM, BAM, File, Explain

    2590 days ago