Results for "R"
Bio-Scripts
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\w+)/; $count_of{$...1915 days ago
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1848 days ago
- my @tests = ( ["FOO", "BAR"], ["CRATE", "TRACE"], ["CRATE", "CRATE"], ["TRACE", "CRATE"], ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], ); for my $word_pair (@tests) {...
1814 days ago
- ...an sudo apt-get install ncbi-blast+ CentOS # download latest BLAST version wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.8.1+-x64-linux.tar.gz # decompress tar -zxvf...
1776 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands 3315 mutate....tant153CH101.fasta > allPalindromeSimulated.fa 3319 ~/Tool...250 -f 100 -m 300 -s 10 -o paired_dat 3321 ~/Tools/seqtk/s...assemble -o seePlatanus -f paired_dat[12].fq -t 101750 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file...Options: -c / --cwd= directory Change working directory -r / --resume...-v / --version Print version and exit...1748 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1739 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1739 days ago
- #!/bin/bash cd `pwd` perl ~/apps/SSPACE-1.2_linux-x86_64/SSPACE_v1-2.pl \ -l libraries.txt \ -s Contigs_over200_nocp.fasta \ -k 5 \ -a 0.7 \ -x 1 \ -m 30 \ -o 20 \ -b Rayk31_scaffolds_extension
1737 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref) = parse_genome_files($ARGV...touch( "$chr_set.out", $chr_seq ); print "finished r...sequence_data{$accession_number}{problem_desc} = "-"; #everyb...1701 days ago
