Results for "End of Evolution"
Bio-Scripts
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both fil...ent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads...2069 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...
2019 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 { pri...
1620 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...1618 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...1571 days ago
- let width = $(window).width() -...t svg = d3.select("body") .append("svg") .attr('id', '...{ source: { id: 'january', start: 1, end: 12 }, target: { id: 'april',..._data, configuration) instance.render()...
1540 days ago
Pack a perl program with their dependencies on Ubuntu !
...package lists... Done Building dependency tree Reading stat...y‐expressed A. gambiae genes is appended below. Biotechnology El...enomes, enabling new insights into evolution and sequence... Latest...gdblab.com - GSP4PDB is a user-friendly and efficient application to sear...1527 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT...============================ Anaconda End User License Agreement =====...s of its c ontributors may be used to endorse or promote products deriv...15.46-py37h14c3975_0 ... installing: send2trash...1527 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print tou...$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""), $0);N++;next;} {printf("%s",$0);} END {prin...1373 days ago
Steps to install Conda on Linux !
Download the installer: Miniconda installer for Linux. ( https://docs.conda.io/en/....sh #Follow the yes/no flags and finish till the end #Check the installation $...ate --name envname # Remove environment and its dependencies...1198 days ago
