Results for "split reads"
Bio-Scripts
Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam1724 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(){chomp; @s = split...
1603 days ago
Samtools commands for bioinformatician !
...le into fasta samtools fasta reads_mapped.sam > reads.fasta #..._sej.bam | less ### sort reads by flag specified and show th...sej.bam | less ### count reads (-c) by flag specified samto...le has two columns: QC-passed reads and QC-failed reads # and ro...1602 days ago
Bash script to download SRA file !
...sequencing run ID fastq-dump --split-files SRR1770413 #SRA stor...ASTQ for further processing. The --split-files part of the command ens...e.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR1770413/SRR1770413.sra sra-dump --split-files SRR1770413.sra1558 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \...#alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and also "give the reads the...n to BAM: samtools view -b - --- this reads SAM from stdin (the - specifi...1558 days ago
To convert just one specific read group to fastq
...> selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data fo...t | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a direct...m # Reverting the process is to extract reads, tagged with readgroups to pa...1541 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1512 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@...maticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents...valuation of genome assembly software based on long readsBy BioStar 409 days ago...1510 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1399 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectIns...1336 days ago
