Results for "Fasta"

Tags

  • 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

    2307 days ago

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

    Tags: duplicate, fasta, ids

    2299 days ago

  • 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

    2296 days ago

  • 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

    2267 days ago

  • #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

    2197 days ago

  • 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

    2172 days ago

  • 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

    2172 days ago

  • #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

    2116 days ago

  • 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

    2106 days ago

  • 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

    1973 days ago