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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

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

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

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 flags https://broadinstitute.github.io/picard/explain-flags.html #SAM #Flags

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

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

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

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