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• • Manisha Mishra@manisha

  

  Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

  2219 days ago

• • Shruti Paniwala@shruti

  

  Finding coding regions in DNA sequences http://genome.crg.es/courses/Lisbon04/exercises/day2/Perl_programming/index.html #Perl #Genes #Script

  2164 days ago

• • Jit@jit.aber

  

  To upgrade the perl in Linux $ sudo cpan; cpan[1]> upgrade #Perl #Upgrade #Linux #Ubuntu

  2160 days ago

• • Jit@jit.aber

  

  perl -pe 's/[^AGTC\n]/N/gi unless m/>/;' /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta > /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds_corrected.fasta #Remove #Non-ATCG

  2152 days ago

• • Jit@jit.aber

  

  perl -e '$/="\n>"; while (<>) { s/>//g; my ($id, $seq) = split /\n/; print ">$_" if length $seq; }' < all_p_ctg.fasta > all_p_ctg_corrected.fasta #Convert #Fasta #Zero

  2148 days ago

• • Jit@jit.aber

  

  Unmask lowercase. perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #LowerCase #Unmask

  2136 days ago

• • Jit@jit.aber

  

  Replace lowercase to N. perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Mask #Lowecase2N #LowerCase

  2136 days ago

• • Jit@jit.aber

  

  perl -pe '/^>/ ? print "\n" : chomp' LR.fasta | tail -n +2 > out.fasta #singleLine #Multifasta #Multi2Single

  2105 days ago

• • Rahul Nayak@rahul

  

  Multi-line fasta to single line fasta $ perl -pe '/^>/ ? print "\n" : chomp' in.fasta | tail -n +2 > out.fasta #Multiline #Singleline #Fasta

  2078 days ago

• • Jit@jit.aber

  

  Rename the fasta header perl -ane 'if(/\>/){$a++;print ">LR$a\n"}else{print;}' allPacBio_clean.fa > allPacBio_clean_shortName.fa #fasta #header #rename

  2020 days ago

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