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...1990 days ago
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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_...1687 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 script1616 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into...sal_sej.bam ### sorting bam file by genome position samtools sort sal_s...x sal_sej_sorted.bam.bam ### identifying genome variants (mpileup command) #...1603 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_1.fastq...is marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same cr...1559 days ago
Perl script to delete the adjacent repeats !
/usr/bin/perl #Mostly the interview question for bioinfomatician ! #Write a code to delete the adjacent repeated character .... $string='ATTTTTTGGC'; # This sho...1551 days ago
Exit Bash Script When Any Command Fails
This can actually be done with a single line using the set builtin command with the -e option. #1--------------------------------------------------------------------...1521 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine do...use all processes within one or more containers port List port mappings or a specific mapping for the container ps...1514 days ago