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Results for "FASTA"

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  • Radha Agarkar

    Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

    Tags: fasta, remove

    2329 days ago

  • Surabhi Chaudhary

    Remove the unwanted characters from Fasta file: sed -e '/^[^>]/s/[^ATGCatgc]/N/g' infile.fa #sed #unwanted #illegal #remove #correct #fasta #linux

    Tags: sed, unwanted, illegal, remove, correct, fasta, linux

    2328 days ago

  • Poonam Mahapatra

    Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa #duplicate #fasta #ids

    Tags: duplicate, fasta, ids

    2321 days ago

  • Jit

    awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

    Tags: remove, empty, clean, fasta

    2318 days ago

  • Rahul Nayak

    #Convert #fasta file to uppercase/lowercase, without altering the annotation line $ awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' name.fasta

    Tags: Convert, fasta

    2219 days ago

  • Manisha Mishra

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

    Tags: extract, fasta, sequence, ids

    2194 days ago

  • Manisha Mishra

    Remove the sequence by fasta ids. awk 'BEGIN{while((getline<"ids.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa #Remove #Delete #ids #fasta

    Tags: Remove, Delete, ids, fasta

    2194 days ago

  • Neelam Jha

    #Convert a #multi-line #fasta to a #singleline #fasta $ awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

    Tags: Convert, multi, fasta, singleline, fasta

    2138 days ago

  • Aaryan Lokwani

    Sed illegal charters from fasta. $ sed '/^[^>]/ s/[^AGTC]/N/gi' < seq.fa #fasta #otherthanATGC #replace #sed #Linux #illegal

    Tags: fasta, otherthanATGC, replace, sed, Linux, illegal

    2128 days ago

  • Jit

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

    Tags: fasta, header, rename

    1995 days ago

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