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_es...reads to be used in the run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m -mer-len...2273 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, '2181 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2266 days ago
Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2266 days ago
Perl script to count the number of files in a directory with regex
..."_E3T1_","_HPRIM14_","_H158_"); my @files = glob("*.scf *.SCF"); foreach my $name (@allNames) { my $nName=lc ($name); my $cnt=0; foreach my $file (@files) { #print "$file =~ /$nName/\n"; my $...2264 days ago
Perl script to read multi fasta sequence one by one
...open (OUT, ">$outfile") or die "couldn't open the file $outfile $!"; print OUT "$key\n$fastaSeq{$key}\n"...my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences;...2248 days ago
2237 days ago
2237 days ago
Biological Sequence handling with Perl !
...nd); if (ref($new_seq)) { croak "argument to concatenate must be a stri...::Nucleotide::Subsequence; use Sequence::Alignment; use Carp; use strict; u...q if ref($seq); return new Sequence::Alignment(src=>$seq,target=>$self->seq)...2208 days ago
Perl script to check fastq reads qualities !
...(($name, $seq, $qual) = readfq(\*STDIN, \@aux)) { ++$n; $slen += length($seq); $qlen += length($qual) if ($qual); print join("\t", $n, $slen, $qlen), "\n"; } #print join("\t", $n, $slen, $qlen),...2181 days ago