Plot custom gene density with R
library(karyoploteR) pp2248 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_rea...ore, where "?" = 30 jellyfish histo -o 19mer_out.histo 19mer_out #Plot dataframe19...2244 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 $fh, '2153 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if...qlen), "\n"; __END__ my @aux = undef; # this is for keeping intermediate data while...2153 days ago
Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forg...busco=4.0.6 Collecting package metadata (repodata.json): done Solving environm...pan-meta-yaml-0.018-pl526_0 perl-data-dumper bioconda/linux-64::p...bioconda/linux-64::perl-module-metadata-1.000036...1451 days ago
2150 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2182 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'} = $sel...2179 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 m...2139 days ago
2125 days ago