Results for "NGS data analysis"
Bio-Scripts
Plot custom gene density with R
library(karyoploteR) pp2242 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read...core, where "?" = 30 jellyfish histo -o 19mer_out.histo 19mer_out #Plot datafram...2239 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2147 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@...n), "\n"; __END__ my @aux = undef; # this is for keeping intermediate data...2147 days ago
Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge...busco=4.0.6 Collecting package metadata (repodata.json): done Solving environm...cpan-meta-yaml-0.018-pl526_0 perl-data-dumper bioconda/linux-64::p...~ bioconda/linux-64::perl-module-metadata-1.0...1446 days ago
- ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomf...ry.h... yes checking for strings.h... yes checking for inttyp...thing to be done for 'install-data-am'. make[2]: Leaving direct...thing to be done for 'install-data-am'. make[2]: Leaving direct...ry.h... yes checking for strings.h......
2144 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; use...} else { croak "Doesn't look like sequence data" unless $sequence=~/^[gactnu\s]+$/i; $self->{'data'} =...2174 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the ref...2133 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [opt...plitting Sequence data may be used in raw form or...Filter used in early 1000 Genomes data: no...Output to stdout, all split data bec...
2119 days ago
Install Parrot Virtual Machine !
...no. auto::coverage - Are coverage analysis tools installed...Negati...builtin_expect.........yes. auto::warnings - Detect supported compiler warnings.................done. gen::co...::config_pm - Record configuration data for later retrieval......done. O...1530 days ago
