Results for "Paired end sequencing"
Bio-Scripts
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-M...=========================== Anaconda End User License Agreement =====...of its c ontributors may be used to endorse or promote products deriv...5.46-py37h14c3975_0 ... installing: send2trash-...1533 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print tou...$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""), $0);N++;next;} {printf("%s",$0);} END {print...1379 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to asse...T AGCCGGACCT TATGATCATT TCATTAGGCG AGGCGGAGCT HINT: There is NO sequencing errors HINT: Overlaps are...
1237 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikr...GB_201904.tgz (JitMetaENV) ➜ day3 mkdir krakenDB (JitMetaENV) ➜ day3 cd krakenDB (JitMetaENV) ➜ krakenDB ls...astq-input --report evol1 --gzip-compressed --paired ../...1236 days ago
Steps to install Conda on Linux !
Download the installer: Miniconda installer for Linux. ( https://docs.conda.io/en/....sh #Follow the yes/no flags and finish till the end #Check the installation $...ate --name envname # Remove environment and its dependencies...1204 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple;...}; #exit 1; } # end 'if' else { print "\n Module $_ OK!\n";} } # end 'for' } # end 'BEGIN' block...B/' ); #Install diamondDB __END__ #...1182 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive:..._ NOT OK!\n }; #exit 1; } # end 'if' else { print "\n Module $_ OK!\n";} } # end 'for'...
1180 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the..._ NOT OK!\n }; #exit 1; } # end 'if' else { print "\n Module $_ OK!\n";} } # end 'for'...1177 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1018 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/rand...=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length...=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length...ixed.fa, out=reads_BBMAP250.fq, pai...LITY=true REPLACE_NOREF=false paired=tru...1012 days ago
