picard tools command to get some insert statistics
...dule load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectInsertSizeMetrics MINIMUM_PCT=0 HISTOGRAM_FILE=.pdf INPUT= OUTPUT=.sorted.collectInseSize HIST...1343 days ago
Download the genome from NCBI using bash script/command
...me" # take action on each file. $f store current file name wget --input $f #cat $f cd .. done #Reference #ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_Downloading...2538 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2531 days ago
Download the gff files from NCBI using bash script/command
...nding G mkdir "GFF$filename" cd "GFF$filename" # take action on each file. $f store current file name head -n 4 $f > $f.head wget --input $f.head gunzip *.gz #c...2529 days ago
Genetic Algorithms demonstration with word DNA in Perl
...foreach my $individual (@$population) { # set the fitness...; my $pop_size = scalar @$population; # population size...dividual $individual = $population->[int(rand($pop_size))]...eration, scalar @sorted_population, dna_to_words($sor...2378 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorte...2320 days ago
Create genome scaffolding with Perl
...; # process remaining command line arguments (hopefully only PSL files) while (@ARGV) { my $argument = shift @ARGV; if(-f $argument){ push (@pslFiles, $argument);...2314 days ago
Plot the clock using Lastz -gerenal outfile
...} foreach my $val (keys %pHash) { #next if $pHash{$val} > 10; my @sChr = split '\_', $val; my $score=$pHash{$val}/$sChr[1]; push @allKeys, $sChr[0]; push @allFreq, $score; } my...2305 days ago
Estimate Genome Size with Jellyfish and R
...both strands #-m -mer-len=unit32 Length of the k-mer #-s -size=unit32 Hash size / memory allocation #-o -output=string Output file name #--min-quality-ch...2252 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2245 days ago