1727 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_geno...1688 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 script1617 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...ols index sal_sej_sorted.bam.bam ### identifying geno...1605 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.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambamb...1561 days ago
1526 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/...r & answer key is released... Evaluation of genome assembly software based on lo...eadsBy BioStar 409 days ago Evaluationgeno...1513 days ago
1511 days ago
Install Ragout genome assembler
$ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home...1466 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/01/2020, 05:30:00 ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00 0 B 10/02/2012, 05:30:0...1404 days ago