Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2245 days ago
Biological Sequence handling with Perl !
...eq($frame,$l-($l-$frame+1)%3) : $self->reverse->subseq(abs($frame),$l-($l-abs($frame)+1)%3); my $s = $seq->seq; $s=~tr/T/U/; # put it in RNA mode $s =~ s/(\...2187 days ago
Perl script to find coding regions in DNA sequences
...perl -w use strict; # if the number of input arguments is lower than 2 #...y @codons to store all of the codons in # the input DNA sequence. To split the s...riplet, the ratio between # the probability computed from the table of codon fr...2161 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paired r...2130 days ago
2157 days ago
2150 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...en2_rev) {$val_rev = $trimLen1_rev; } elsif ($trimLen1_rev (\S+)(.*)/) { $seqid = $1; $sequences{$seqid}{desc} = $2; push @allIds, $seqid; }...2146 days ago
Perl script to run SATSUMA in loop !
...atsumaLoc="/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the...2146 days ago
Perl script to convert GFF 2 FASTA !
...Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqI...ormat => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type description ###### # c...2145 days ago
2133 days ago