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...1585 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-----------------------------------------------------------------------...1563 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web ji...A is a method for detecting structural variants in sequencing data using genome-wide local...ansfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularl...1554 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1443 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS="...{print $0}' input1.fasta input2.fasta #Merge all FASTA files in a directory into a single FAS...1400 days ago
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Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.nc...986 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa971 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To use Varscan we simply need to d...866 days ago