Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2062 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 > toyheterozyg...2059 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment:...22 KB bioconda pbcommand-1.1.1 |...1.3 MB bioconda mkl_random-1.0...._1 bioconda pbcommand:...information on License, Copyright and Discla...1996 days ago
1732 days ago
Perl script to run in parellel !
...($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref}; my...processes ) { $pm->start and next; my $count = 0; foreach my $chr_set (keys %genome) { $count++...LE or die $!; } sub parse_genome_fil...1693 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 script1622 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam...# viewing bam files (view command) samtool view sal_sej.bam |...sort reads by flag specified and show them # -f INT show flag...ed.bam.bam ### identifying genome variants (mpileup command) # -g : output is bcf (binary c...1609 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired F...ectly downloading data from a particular sequencing...ssing. The --split-files part of the command en...ures we get two files, one for the first and second mate in each pair. We'll use...1566 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_...--- this says "align using so many threads" and also "give the reads the read group K12 and th...er in place of the file name indicates this) and conver...1566 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # Th...1549 days ago