BOL

Log in

Our Sponsors


Download BioinformaticsOnline(BOL) Apps in your chrome browser.


Results for "FASTA"

Tags

  • Jit

    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

    3628 days ago

  • Jit

    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

    3570 days ago

  • Rahul Nayak

    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

    3182 days ago

  • Rahul Nayak

    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

    3154 days ago

  • Rahul Nayak

    Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #Perl #Oneliner #Trick #Tips #Fasta #Identifier #Remove

    Tags: Perl, Oneliner, Trick, Tips, Fasta, Identifier, Remove

    3154 days ago

  • Abhimanyu Singh

    fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #Convert #Fasta #Fastq #fa #fq

    Tags: Convert, Fasta, Fastq, fa, fq

    2544 days ago

  • Neelam Jha

    Delete space from FASTA header: perl -pe 's/>\S+\K.+//' < file.fasta > new_file.fasta #PerlOneLiner #Trick #Perl #Space #Fasta

    Tags: PerlOneLiner, Trick, Perl, Space, Fasta

    2973 days ago

  • Radha Agarkar

    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

    Tags: Perl, PerlOneliner, PerlTrick, Extract, Ids, Fasta

    2782 days ago

  • Shruti Paniwala

    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

    Tags: Samtools, Fasta, Extract, Multifasta

    2742 days ago

  • Jit

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

    Tags: Fasta, Bed, Coordinates, Bedtools

    2609 days ago

Powered by Elgg