Installing Porechop on Ubuntu !
...[--end_threshold END_THRESHOLD] [--no_split] [--discard_..._MIDDLE_TRIM_BAD_SIDE] [--min_split_read_size MIN_SPLIT_READ_SIZE...(default: reads with middle adapters are split) (...2118 days ago
2087 days ago
Perl script to extract a sequence from multifasta with range !
...parameter not provided\n"; { local $/=">"; while() { chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = s...2078 days ago
Perl script to break the contigs by 'N'
...the end of the NNNNN region in the contig my @regions=(); my @bases=split //,$seq; push(@bases,"E");...#regions]; # print "$lastregion $#regions\n"; die; my ($ini,$end)= split /\s+/,$lastregion; if (($e...2074 days ago
Perl script to split fasta sequence / overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2055 days ago
Perl script to create a consensus of nucleotide sequences !
...foreach my $j ( 0 .. $w-1 ){ # Initialize the base counts. my %h = ( a=>0, t=>0, c=>0, g=>0 ); my @mi_letters = map { [split '', uc $_] } @mi; foreach...2044 days ago
2046 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "1984 days ago
Split the multifasta in separate files !
cat Avaga_allPalindrome.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'1969 days ago
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\w...1912 days ago