Results for "Paired end sequencing"
Bio-Scripts
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->...#Each region is represented as a pair "$ini $end" indicating that start and #the end of the NNNNN region in the co...($pseqobj); print SCAFF "$new_id $cini $cend\n";...2085 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both fil...percent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads...2075 days ago
- #!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {print $0}' deduped_MA605.coverage > c...
2026 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth...ength($5)) { SUM+=length($5)-length($4); } else { SUM+=length($4)-length($5)}} END { prin...
1626 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting s...ls depth -a sorted_dupremoved.bam | awk '{c++;s+=$3}END{print s/c}' ### one liner...orted_dupremoved.bam | awk '{c++; if($3>0) total+=1}END{print...1625 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fast...he SRA toolkit. It allows directly downloading data from a particular sequencing run ID fastq-dump --split-...1581 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O http...>>> =================================== Anaconda End User License Agreement =====...uamel_yaml-0.15.46-py37h14c3975_0 ... installing: send2trash-...1577 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197...everting the process is to extract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1...1564 days ago
- let width = $(window).width() -...svg = d3.select("body") .append("svg") .attr('id', '...{ source: { id: 'january', start: 1, end: 12 }, target: { id: 'april',...data, configuration) instance.render()...
1546 days ago
Pack a perl program with their dependencies on Ubuntu !
...ressed A. gambiae genes is appended below. Biotechnology El...ab.com - GSP4PDB is a user-friendly and efficient application t...ecting structural variants in sequencing data using genome-wide local...n bacteria using whole-genome sequencing (WGS) data. It is particularl...1533 days ago
