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Results for "structural and sequence variation"

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• • Shruti Paniwala@shruti

  

  Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

  2657 days ago

• • Jit@jit.aber

  

  AVID: A Global Alignment Program https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/ #AVID #Alignment #Global #Sequence #Genome

  2625 days ago

• • Jit@jit.aber

  

  Whole-Genome Sequencing (WGS) PPT http://www.bx.psu.edu/~ratan/Sequence%20Analysis.pdf #PPT #WGS #Ratan

  2619 days ago

• • Jit@jit.aber

  

  Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools

  2613 days ago

• • Abhimanyu Singh@abhimanyu

  

  #Extract a #sequence from #multi-fasta file: $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file

  2608 days ago

• • Abhimanyu Singh@abhimanyu

  

  #Random #sequence generator with #perloneliner : $ perl -e '$x=int(rand(1000)); printf( "chr1\t%s\t%s", $x, $x + 10)'

  2608 days ago

• • Jit@jit.aber

  

  Beginner’s #guide to #comparative #bacterial genome #analysis using #next-generation sequence data https://microbialinformaticsj.biomedcentral.com/articles/10.1186/2042-5783-3-2

  2499 days ago

• • Jit@jit.aber

  

  Rename #non-accepted #nucleotide from sequence to 'N' $ bbmap/reformat.sh in=genome.fa out=genomeOut.fa iupacToN=t

  2485 days ago

• • Neelam Jha@neelam

  

  Reformat you fasta sequence with size. $ seqkit seq -w 50 allGenomeContacted.fa > allGenomeContacted_final.fa #Reformat #Fasta #Size

  2466 days ago

• • Jit@jit.aber

  

  #Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

  2332 days ago

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