BOL: Wire posts tagged with 'Bam'

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

Wire post by Jit

Jit — Wed, 19 Dec 2018 03:58:11 -0600

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

Wire post by Jit

Jit — Wed, 28 Nov 2018 10:31:56 -0600

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

Wire post by Neel

Neel — Thu, 18 Oct 2018 09:00:03 -0500

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

Wire post by Neel

Neel — Fri, 12 Oct 2018 08:12:05 -0500

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

Wire post by Jit

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

Wire post by Jit

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

Wire post by Jit

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

Wire post by Jit

Jit — Tue, 28 Feb 2017 09:07:34 -0600

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

Wire post by Jit

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

Wire post by Shruti Paniwala

Shruti Paniwala — Tue, 25 Oct 2016 05:25:43 -0500

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

Wire post by Jit

Jit — Mon, 18 Jul 2016 10:08:21 -0500

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

Wire post by Jit

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

Wire post by Jit

Jit — Mon, 27 Jun 2016 08:39:50 -0500

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

Wire post by Poonam Mahapatra

Poonam Mahapatra — Fri, 24 Jun 2016 09:16:32 -0500

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