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Results for "fasta"

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  • 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

    2334 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

    2331 days ago

  • Neelam Jha

    Converting FASTQ to FASTA

    There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence need...

    Tags: fasta, fastq, convert, sed, awk, seqtk, bioawk, fastx, Emboss, fastq2fasta

    2302 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

    2232 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

    2207 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

    2207 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

    2151 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

    2141 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

    2008 days ago

  • Rahul Nayak

    Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

    Tags: fasta, header, add, number, count

    1960 days ago

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