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• • Neelam Jha@neelam

  

  PAired-eND Assembler for DNA sequences https://github.com/neufeld/pandaseq #Sequence #Assembler #PANDAseq

  2945 days ago

• • Radha Agarkar@radhaagarkar

  

  Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta

  2782 days ago

• • Radha Agarkar@radhaagarkar

  

  Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file #PerlTricks #PerlOneliner #Perl #Extract #Ids #

  2782 days ago

• • Shruti Paniwala@shruti

  

  Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

  2742 days ago

• • 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

  2653 days ago

• • Jit@jit.aber

  

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

  2621 days ago

• • Jit@jit.aber

  

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

  2615 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

  2609 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

  2604 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)'

  2604 days ago

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