Results for "NT"
Bio-Scripts
...elp gatk --list Print the list of available tools...raw Illumina sequencing data into an unmapped SAM or BAM file....Produces a summary of alignment metrics from a SAM or BAM fil...card) Identifies duplicate reads....2127 days ago
- ...zsh Updating Oh My Zsh remote: Counting objects: 484, done. remot...+++++++++++++--------- plugins/frontend-search/README.md...| 12 ++-- plugins/frontend-search/frontend-search.plu...| 22 +++--- plugins/ssh-agent/README.md...
2126 days ago
Perl script to extract a sequence from multifasta with range !
...rl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $...ift @chunk; my $seqlen = length join "", @chunk; print ">$_" if($seqlen >= $minlen a...2118 days ago
Perl script to break the contigs by 'N'
...my $seqobj = $fasta->next_seq() ) { #gets contig id my $contig = $seqobj->display_id();...ks) #Hash nregions stores a hash from the contig id to the NNNNN regions fou...ll regions without Ns are in @regions my $cont=1; my $laststart=1; if ($...2114 days ago
- library(vcfR) # Input the files. vcf
2112 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2107 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent.fasta #generated 50X of Il...2105 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 $fh, "2095 days ago
Perl script to reverse complement a DNA sequence !
...ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; print "Here is the starting DNA:\n\n"; print "$DNA\n\n"; $revcom = reve...om =~ s/G/C/g; $revcom =~ s/C/G/g; print "Here is the reverse compleme...$revcom =~ tr/ACGTacgt/TGCAtgca/; print "Here is the reverse compleme...2095 days ago
Installing pb-assembly on Linux !
...netcdf/intel/64/3.6.0 expat/2.2.0-foss-...Perl/5.24.0-foss-2016b Geant4/9.5.p01-goolf-1.4.10...for installation in environment /home/unamur/URBE/jnarayan/.c...70a237_1 bioconda python-intervaltree 2.1.0...2086 days ago
