Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2457 days ago
Convert fastq to fasta in Perl
use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq'); my $out=Bio::SeqIO->new(-...2320 days ago
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Perl script to convert fastq to fasta file
...y->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object $seqret->run({-sequence => $infile, -sformat1 => 'fastq', -outseq =>...2240 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read_2.fastq #-t -treads=unit32 Nu...2235 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...2143 days ago
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