Results for "NT"
Bio-Scripts
Perl script to find coding regions in DNA sequences
...1); } # create two vars contaning the filenames my $fil...e frequencies of codon usage into the hash table %pcodons # t...CE,"< $filesequence")) { print "dnaloglkh.pl: the file $file...64); $i = $i + 1; } printf "%.2f\n",$r; __END__...2197 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
.... 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 --threads N where N is an integer specifying how many threa...2166 days ago
- ...gsc/bloomfilter.git Cloning into 'bloomfilter'... remote: Counting objects: 867, done. remot...Tests configure.ac nthash.hpp ➜ bloomfilter git:(...ake all-recursive make[1]: Entering directory '/home/urbe/To...tall in Tests/Unit make[1]: Entering directory '/home/urbe/To...
2194 days ago
- ...e already installed these essentials: # Debian/Ubuntu system admins should run: s...re you want to install different Perls, and cd into it: # Not...n-standard location is baked into the perl binary: cd perl-5....~/.bashrc` to make it persistent. # But be sure to define `$P...
2187 days ago
Perl script to count number of Ns in a multifasta file !
...str($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($...__END__ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backu...2187 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2187 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...see the distance beetween all the contigs and scaffolds #Usage: per...foreach my $chr (@$SeqIds) { my $cnt=0; my $value=scalar(@$SeqId...ile); next if $chr eq @$SeqIds[$cnt]; print "$chr\t@$SeqIds[$c...= hammingDist($seq1, $seq2); print "$val\n"; }} until($value=...2183 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 he...2183 days ago
Perl script to convert GFF 2 FASTA !
...tion ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but containing untranslated exons) #...2181 days ago
Long reads mapper bash script !
....sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scri...]; then echo "No or less arguments provided" echo "#USAGE:...le used for mapping $fileName, present at $refFasta" if [ $toolNa...INIMAP2:Please specify reads type: ont, pacbio" fi elif [ $toolNa...2165 days ago
