Results for "1"
Bio-Scripts
zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc2220 days ago
Biological Sequence handling with Perl !
...ppend . $self->seq : $self->seq . $to_append); } 1; Back to Article Listin...shift; return (__PACKAGE__ . '::Subsequence')->new($self,$self->length,1); } sub translate { my $...2191 days ago
Perl script to check fastq reads qualities !
...defined(@$aux)); return if ($aux->[1]); if (!defined($aux->[0]))...) { chomp; if (substr($_, 0, 1) eq '>' || substr($_, 0, 1) e...n; } } my $name = /^.(\S+)/? $1 : ''; my $seq = ''; my $c...ame, $seq, $qual); } } $aux->[1] = 1; return ($name, $seq);...2164 days ago
Perl script to find coding regions in DNA sequences
...l codontable DNAsequence\n"; exit(1); } # create two vars con...$ARGV[0]; my $filesequence = $ARGV[1]; # open the first file:...equence can not be opened\n"; exit(1); } # FASTA format: #...ndom probability (uniform), that is, 1/64. After this, # the log mu...2165 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...ed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta -...2134 days ago
- ...remote: Compressing objects: 100% (11/11), done. remote: Total 86...+ automake -a configure.ac:19: installing './compile' con...install in Tests/AdHoc make[1]: Entering directory '/home/u...ess install-sh stamp-h1 config.h KmerBloomFilter....
2162 days ago
- ...t install -y build-essential libexpat1-dev libssl-dev libmysqlclient...rl --create-dirs -L -o src/perl-5.24.1.tar.gz http://www.cpan.org/sr...into the perl binary: cd perl-5.24.1 ./Configure -des -Dprefix=$P..." export PATH="$PERL_BASE/perl-5.24.1/bin:$PATH" # You can add t...
2154 days ago
Perl script to count number of Ns in a multifasta file !
...countN.pl out.fasta scaffold1_size15575755 15575755 71824 0...affold3_size10490233 10490233 14872 0.0014197124089566 scaff...6206 2236206 132012 0.0627375612704912 scaffold15_size218421...scaffold38_size462550 462550 16583 0.0371843656593425 scaff...2154 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...e warnings; use Bio::SeqIO; $| = 1; #Script to see the distan...$SeqIds); do{{ $value=$value-1; my $ofh = write_fh($tmpFi...$cnt++; system ("mafft --retree 1 --maxiterate 0 --thread 40 $t...l($value= $trimLen2) {$val = $trimLen1; } elsif ($trimLen1 = $trimLe...2150 days ago
Perl script to run SATSUMA in loop !
...r/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis #...ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #...2150 days ago
