Results for "fasta"
Bio-Scripts
Perl script to find the distance beetween all the contigs and scaffolds
...ome.fa > HammingDist.txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]); my $tmpF...t"); #usage: perl clustalRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2hash('MAFFT_out'); m...2134 days ago
Perl script to run SATSUMA in loop !
...use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarf...2134 days ago
Perl script to convert GFF 2 FASTA !
...eq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output...cds = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cds.fas...> 'fasta', -file => ">$ARGV[2].pep.fasta" ); my $outfile_cdna = Bio::..., -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type des...2133 days ago
- ...3.2.3/config #run BUSCO python BUSCO.py -i /media/urbe/MyDDrive/longMIRA_canuCorrect_sspaceLong/GRAAL_Haploid/adineta_p_lvl6/genome_CORRECTED2.fasta -c 30 -l metazoa_odb9 -o GRAA...
2131 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($_ =~ /^>/){...2127 days ago
- ...inity-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads le...inity-v2.6.6/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads ri...-Trinity-v2.6.6/Chrysalis/GraphFromFasta -i /home/urbe/Tools/trinityrn...ed transcripts into a single multi-fasta file... Monday, July 9, 20...
2121 days ago
- ...iD). Quality -Q|--offset Offset to use for quality conversion, default is 33 --fasta FASTA only, no qualities, optional...
2120 days ago
- ...--assembly= Assembly file(s) in FASTA format, comma-separated --...Reference proteome or transcriptome file in FASTA...a/urbe/MyPassport/BorisTrinityAssembly/Trinity.fasta [ INFO] 2018-07-13 14:54:21...
2117 days ago
Installing Porechop on Ubuntu !
...ipt to /home/urbe/anaconda3/bin ➜ Porechop git:(master) porechop -h usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]...2100 days ago
Perl script to extract sequence by Ids from multifasta file !
...$ids{$_} += 1; } close FILE; local $/ = "\n>"; # read by FASTA record open FASTA, $seqfile; while () { c...# remove endlines print ">$id\n$seq\n"; } } close FASTA;...2090 days ago
