Results for "FASTQ"
Bio-Scripts
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);2452 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 $out=Bio::SeqIO->new(-...2314 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2248 days ago
- # bash cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr...print;}' > file.fa #seqtk seqtk seq -a input.fastq > output.fasta #Bioawk bioawk -c fastx '{print ">"$name"\n"$seq}' input.fastq > output.fasta #Sed sed -...
834 days ago
Perl script to convert fastq to fasta file
...y->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication object $seqret->run({-sequence => $infile, -sformat1 => 'fastq', -outseq =>...2235 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_read_2.fastq #-t -treads=unit32 Nu...2230 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...2138 days ago
- ..._C1CBGACXX.IND11_noribo_clean.fastq --CPU 40..._C1CBGACXX.IND11_noribo_clean.fastq' ]; Right read file..._C1CBGACXX.IND11_noribo_clean.fastq' ], [..._C1CBGACXX.IND11_noribo_clean.fastq.normalized_K25_maxC50_minC1_p...
2111 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...] ./fastq-dump [opt...conditions are placed in files *_1.fastq and...present it is placed in *.fastq Biological...
2110 days ago
- ...format, comma-separated --left= Left reads file(s) in FASTQ format, comma-separated --right= Right reads file(s) in FASTQ format,...
2107 days ago
