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• • Jitendra Narayan@admin

  

  A perl tool to conveniently parse RepeatMasker output files http://www.mobilednajournal.com/content/5/1/13 #Perl #Repeat #Transposable #NGS #Genome #TEs #Mobile

  3489 days ago

• • Poonam Mahapatra@poonam

  

  #Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

  2860 days ago

• • Jit@jit.aber

  

  Remove tab with comma in file: perl -lpe 's/\t/,/g' < flattened_line_0.fa.data > output.csv #PerlTrick #PerlO,liner #Perl #Tab #Comma

  2820 days ago

• • Jit@jit.aber

  

  Understanding N50 http://jermdemo.blogspot.be/2008/11/calculating-n50-from-velvet-output.html #N50 #Assembly #Genome #Contigs

  2783 days ago

• • Jit@jit.aber

  

  To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta

  2559 days ago

• • Jit@jit.aber

  

  #Target 4 and #HSPS 1 with #blast $ blastn -task megablast -query brkSeq.fa -db myDBAvaga -evalue 1e-5 -num_threads 1 -max_target_seqs 4 -max_hsps 1 -outfmt '6' -out output

  2532 days ago

• • Radha Agarkar@radhaagarkar

  

  Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

  2332 days ago

• • Neelam Jha@neelam

  

  sed -i -e '/^+/,/^\@/{/^+/!{/^\@/!d}}; /^+/ d; s/@/>/g' OUTPUT.fastq > out.fa #Convert

  2142 days ago

• • Rahul Nayak@rahul

  

  Grep a term from a file in Linux. $ grep -A1 "term" input.fasta > output.fasta #Grep #Term

  1586 days ago