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

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

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

BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

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

Bioinformatics tutorial https://jasonjwilliamsny.github.io/wrangling-genomics/01-automating_a_workflow.html #Workflow #Tutorial #BAM #SAM #SNP

Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

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

Split the bam file by chromosome. $ bamtools split -in file.bam -reference #Split #Bam #Bamtools

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

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

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

Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

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

#Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam