Results for "structural and sequence variation"
Bio-Scripts
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2144 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SAT...Store the ids if ($ARGV[1] eq "ids") { my $idFile="palindrome_ids.txt"; open my $handle, '2140 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::...cription ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but conta...ntire gene sequence (including UTRs and intro...2139 days ago
- ...Remove adapter sequences from reads Common Filter...Dump only unaligned sequences --aligned-region Filte..."chr1" or "1"). "from" and "to" are 1-based...are placed in files *_1.fastq and...
2126 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-...ob Patro, Julian Hibberd, and Steve Kelly DESCRIPTION:...three kinds of metrics: 1. sequence based (if --assembly is...read mapping based (if --left and --right are given) 3. reference b...Show some example commands with...
2123 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1;...2096 days ago
- ...ES/FILE gatk forwards commands to GATK and adds some sugar for submitting spark...---------------------------- Structural Variant Discovery:...tracts evidence of structural variations from reads FindBreakpoi...tural variants StructuralVariationDiscoveryPipelineSpark (BET...
2075 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange....my $seqlen = length join "", @chunk; print ">$_" if($seqlen >= $minlen and $seql...2066 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -...my $contig = $seqobj->display_id(); #gets contig sequence my $seq = $seqobj->seq; m...sented as a pair "$ini $end" indicating that start and #t...2063 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, "2043 days ago
