Results for "genome structure"
Bio-Scripts
➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...]...l-filter Filter used in early 1000 Genomes data: no...ter-1 Filter used in current 1000 Genomes d...2178 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/relea...awWgsMetrics (Picard) Collect whole genome sequencing-related metrics....ct metrics about coverage and performance of whole genome se...
2127 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 > toyheterozy...2105 days ago
- #http://www.nupack.org/downloads/source ➜...s.c pfuncUtils.c: In function ‘PrintStructure’: pfuncUtils.c:950:7: warnin...-Wunused-result] scanf("%s", structure); ^~~~~~~~~~~~~~~~~~~...design_engine.c: In function ‘parseStructure’: design_engine.c:1257:2: wa...
2078 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 Proc...2042 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
1777 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManag...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_fi...1738 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1667 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam...q 42 -c sal_sej.bam ### sorting bam file by genome position samtools sort sal_s...ls index sal_sej_sorted.bam.bam ### identifying genome va...1655 days ago
