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The Wire
#bam
Wire posts tagged with 'bam'
Jit
@jit.aber
Thread
By
Jit
2039 days ago
Get the secondary hists reads count from SAM awk '{ print $2 }' out.sam| grep "2048" | wc -l
#SAM
#BAM
#Secondary
#Hits
Jit
@jit.aber
Thread
By
Jit
2167 days ago
#Split
the
#BAM
file $ /home/urbe/Tools/bamtools/bin/bamtools split -in improved3.fasta.sorted.bam -reference
#bamtools
Jit
@jit.aber
Thread
By
Jit
2187 days ago
Ribbon genomics
http:/
/
genomeribbon.com/
#Visualization
#Ribbon
#Graph
#Genome
#BAM
#SAM
#Mummer
Neel
@neelam
Thread
By
Neel
2228 days ago
BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed
#Bed
#bam
#bamToBed
#convert
Neel
@neelam
Thread
By
Neel
2234 days ago
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
Jit
@jit.aber
Thread
By
Jit
2410 days ago
Bioinformatics tutorial
https:/
/
jasonjwilliamsny.github.io/
wrangling-genomics/
01-automating_a_workflow.html
#Workflow
#Tutorial
#BAM
#SAM
#SNP
Jit
@jit.aber
Thread
By
Jit
2823 days ago
Convert a SAM file to tab-delimited alignment coordinates
https:/
/
gist.github.com/
sjackman/
7016520
#SAM
#BAM
#Convert
#Tab
Jit
@jit.aber
Thread
By
Jit
2824 days ago
SAM and BAM handling with Perl
http:/
/
search.cpan.org/
~lds/
Bio-SamTools/
lib/
Bio/
DB/
Sam.pm
# Perl
#SAM
#BAM
Jit
@jit.aber
Thread
By
Jit
2825 days ago
Split the bam file by chromosome. $ bamtools split -in file.bam -reference
#Split
#Bam
#Bamtools
Jit
@jit.aber
Thread
By
Jit
2830 days ago
Understanding and manipulating SAM/BAM alignment files
http:/
/
homer.salk.edu/
homer/
basicTutorial/
samfiles.html
#SAM
#BAM
#File
#Explain
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2952 days ago
Coverage R Plot
http:/
/
davetang.org/
muse/
2013/
09/
07/
creating-a-coverage-plot-in-r/
#R
#Plot
#Genome
#Image
#NGS
#BAM
Jit
@jit.aber
Thread
By
Jit
3050 days ago
Plot the coverage in R
http:/
/
cnr.lwlss.net/
SeqCoverage/
#BAM
#SAM
#R
#NGS
#Plot
Jit
@jit.aber
Thread
By
Jit
3069 days ago
Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}'
#SAM
#BAM
#Samtools
#Tricks
#NGS
Jit
@jit.aber
Thread
By
Jit
3071 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
Poonam Mahapatra
@poonam
Thread
By
Poonam Mahapatra
3074 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
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