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 # The number of datasets to subselect from the project....1556 days ago
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Exit Bash Script When Any Command Fails
...-------------------------------------------------------------------- # exit when any command fails #Putting this at the top of a bash script will cause the script to exit if any commands retur...1534 days ago
Installing docker for Bioinformatics on Ubuntu !
...jit@jit-HP-Pro-3335-MT:~/Downloads$ chmod 777 get-docker.sh jit@jit-HP-Pro-3335-MT:~/Downloads$ ./get-docker.sh # Executing docker install script, commit: 442e66405c304fa92af8...1527 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1527 days ago
Pack a perl program with their dependencies on Ubuntu !
....8.3-2ubuntu0.1) ... #you can find the test script web.pl at https://bioinformaticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-...ncestubemapgraphmap github.com - A JavaScript module for the visualization...1525 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1229 days ago
Script to extract the cluster detail !
$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ cat /proc/cpuinfo | grep -i 'model name' | head -n 1 model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz1392 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1379 days ago