Results for "FASTA"

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  • GenBank to FASTA format conversion, Written By Junguk HUR http://tinyurl.com/ntp7w5v #Perl #FASTA #Genbank

    Tags: Perl, FASTA, Genbank

    1268 days ago

  • Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. https://github.com/lh3/seqtk #FASTA #FASTAQ #NGS

    Tags: FASTA, FASTAQ, NGS

    1028 days ago

  • zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa #fastaQ2fasta #fastaq #fasta #Oneliner

    Tags: fastaQ2fasta, fastaq, fasta, Oneliner

    1047 days ago

  • perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

    Tags: Perl, Extract, Fasta

    1022 days ago

  • Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter. #Vim #vi #N #Replace #Fasta

    Tags: Vim, vi, N, Replace, Fasta

    1022 days ago

  • Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner

    Tags: Delete, Space, Fasta, Perl, Oneliner

    1022 days ago

  • FastaQ 2 Fasta Oneliner: paste - - - -< totalRNA_placental_1.fastq | perl -pale'$_="@F[0..1]"'|tr "\^@" "\>" | perl -pale 's/\s/\n/g' #Oneliner #NGS #FastaQ #Fasta

    Tags: Oneliner, NGS, FastaQ, Fasta

    1035 days ago

  • To count number of fasta entries, I use: grep -c '^>' mySequences.fasta #Perl #Count #Number #Fasta #Linux #Grep

    Tags: Perl, Count, Number, Fasta, Linux, Grep

    976 days ago

  • Sort FASTA sequence by length: cat f1.fasta| awk '{if($0 ~ /^>/){printf "%st", $0}else{print length($0)"t"$0}}'| sort -k2n,2| awk '{print $1"n"$3}' > sequence.fasta #Sort #Fasta #Trick #Onliner

    Tags: Sort, Fasta, Trick, Onliner

    589 days ago

  • Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.txt sample1.fa #Extract #Sequences #IDs #Fasta #Perl #Trick #Oneliner

    Tags: Extract, Sequences, IDs, Fasta, Perl, Trick, Oneliner

    561 days ago