Results for "Bin"
Bio-Scripts
Install StringTie on ubuntu / Linux !
...assembly and quantification of RNAseq data. The binary distributions are availabl...find. # download and extract cd ~/workspace/bin wget http://ccb.jhu.edu/soft..._64.tar.gz # make symlink ln -s ~/workspace/bin/stringtie-1.3.0.Linux_x86_64/...851 days ago
Install Varscan on Ubuntu / Linux !
...we simply need to download the distributed jar file into our ~/workspace/bin. As with the other java progr...e can invoke Varscan via java -jar. # Install Varscan cd ~/workspace/bin curl -L -k -o VarScan.v2.4.2...851 days ago
- ...ke a symlink so the executable downloaded is available directly from our bin folder. To run GATK we must f...n the command source deactivate. # download and unzip cd ~/workspace/bin wget https://github.com/broa...
839 days ago
- #!/bin/bash #Counting k-mers for different k echo "k,unique,distinct,total" for k in {1..15}; do kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1 egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\ END{print "'$k',"u","d","t}' done
822 days ago
- ...... Setting up libgsl23:amd64 (2.5+dfsg-6build1) ... Setting up art-nextgen-simulation-tools (20160605+dfsg-4) ... Processing triggers for libc-bin (2.31-0ubuntu9.9) ... Proces...
692 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $s...453 days ago
Perl script to find edit distance between two sequences !
#!/usr/bin/perl use strict; use warnings; sub edit_distance { my ($s1, $s2) = @_; my $len1 = length($s1); my $len2 = length($s2); my @dp; for (my $i = 0; $i453 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared test of the dinucleotide frequencies of two FASTA files # Last updated by: $Author$ # Last updat...439 days ago
- #!/usr/bin/env Rscript library(RCircos) # usage: Rscript make_circos.r # parse args args = commandArgs(trailingOnly=TRUE) sv.file
327 days ago
Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) = @_; $sequence = uc($sequence); # Convert the sequence to uppercase my $gc_count = () = $seq...124 days ago
