Results for "data compression"
Bio-Scripts
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_rea...ore, where "?" = 30 jellyfish histo -o 19mer_out.histo 19mer_out #Plot dataframe19...2240 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 $fh, '2148 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if...qlen), "\n"; __END__ my @aux = undef; # this is for keeping intermediate data whi...2148 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-1.0000...1447 days ago
- ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomfilter.git Cloning int...xec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving direct...xec-am'. make[2]: Nothing to be done for 'install-data-am'....
2145 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; us...} else { croak "Doesn't look like sequence data" unless $sequence=~/^[gactnu\s]+$/i; $self->{'data'} = $s...2175 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 reference multifasta file name here...2134 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 become...
2120 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages jit@j...other build files...........done. gen::config_pm - Record configuration data for la...1531 days ago
- # list sample names & download URLs. sample_links = {"ERR458493": "https://osf.io/5d...ES=sample_links.keys() # download yeast rna-seq data from Schurch et al, 2016 stud...nload_all: input: expand("rnaseq/raw_data/{sampl...
1510 days ago
