BOL: Wire posts tagged with 'SAM'

Wire post by Jit

Jit — Thu, 25 Apr 2019 08:43:22 -0500

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

Abhimanyu Singh — Sat, 20 Apr 2019 22:40:22 -0500

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

Jit — Wed, 28 Nov 2018 10:31:56 -0600

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

Jit — Thu, 19 Apr 2018 10:16:44 -0500

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

Jit — Thu, 02 Mar 2017 10:54:53 -0600

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

Jit — Thu, 02 Mar 2017 05:40:01 -0600

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

Jit — Wed, 01 Mar 2017 11:16:44 -0600

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

Jit — Fri, 24 Feb 2017 04:46:36 -0600

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

Jit — Mon, 18 Jul 2016 10:08:21 -0500

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

Jit — Thu, 30 Jun 2016 04:48:56 -0500

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

Jit — Fri, 23 May 2014 10:11:28 -0500

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