Results for "human reference genome"
Bio-Scripts
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($_ =~ /^>...2134 days ago
- ...Filter used in early 1000 Genomes data: no...Filter used in current 1000 Genomes data Filters based on align...between the references. Use from-to to limit...matepair distance on the same reference Filters for individual...
2127 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate...ng based (if --left and --right are given) 3. reference based (if --reference is given) Documentation at...diagnostics [ INFO] 2018-07-13 14:54:34 : No refere...
2124 days ago
- ...(BETA Tool) Collects reference and alternate allele counts a...e GATK's internal pileup to a reference Samtools mpileup CheckTe...Collect whole genome sequencing-related metrics...., soft-clipping beyond-end-of-reference alignments and setting MAP...
2076 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2056 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheteroz...2054 days ago
Perl script to create a consensus of nucleotide sequences !
use strict; use warnings; my @instances = qw ( AAAAA ATCGA ATAAA ); my @instances2 = qw ( AAAAA AACGA ATAAA AGA...{$b} $prefOrder{$a} } qw/A T G C/ ]->[0]; } return @cons; } #refere...2033 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/denovo_asm Pro...1991 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1726 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warning...my ($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref}; my...; foreach my $chr_set (keys %genome) { $count++...e FILE or die $!; } sub parse_genome_files { my $file=shift;...1688 days ago
