Results for "multiple fasta"
Bio-Scripts
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2160 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO;....txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]); my $tmpF...clustalRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2hash('MAFFT_out'); m...2156 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usag...for SATSUMA analysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarf...2156 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warn...use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output...Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cds.fas...sta', -file => ">$ARGV[2].pep.fasta" ); my $outfile_cdna = Bio::...le => ">$ARGV[2].upstream3000.fasta" ); ###### Output type des...2154 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin ex...longMIRA_canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metazoa_odb9 -o GRAA...
2153 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/){...2149 days ago
- ➜ trinityrnaseq-Trinity-v2.6.6 git:(m...-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads le...-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads ri...ity-v2.6.6/Chrysalis/GraphFromFasta -i /home/urbe/Tools/trinityrn...anscripts into a single multi-fasta file... Monday, July 9, 20...
2143 days ago
- ...Compress output using bzip2 Multiple File Options Set...default is 33 --fasta FASTA only, no qualities, optional...am Use multiple times for more verbosity...
2142 days ago
- ...y= Assembly file(s) in FASTA format, comma-separated --lef...proteome or transcriptome file in FASTA...blies= Merge best contigs from multiple assemblies into...port/BorisTrinityAssembly/Trinity.fasta [ INFO] 2018-07-13 14:54:21...
2139 days ago
Installing Porechop on Ubuntu !
...sage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]...Control the binning of reads based on barcodes (i.e. barcode demultiplexing) -b BARCODE_DIR,...2121 days ago
