Results for "sed"

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  • Awk

    Awk

    Awk is widely used these days for extraction and manipulation of large scale biological data in Unix/Linux.Most of the awk code is single liner. Useful Weblinks: http://www.grymoire.com/Unix/Awk.html http://www.hcs.harvard.edu/~dholland/computers/awk.html http://www.pement.org/awk/awk1line.tx...

    Tags: awk, gawk, nawk, sed, data, sequencing, one liner

    1626 days ago

  • #Remove all line that start with # file: $ sed '/^#/ d' filename #line #sed #linux

    Tags: Remove, line, sed, linux

    317 days ago

  • Remove "|" from fasta header. $ sed 's,|,_,g' -i file.fa #fasta #header #sed

    Tags: fasta, header, sed

    189 days ago

  • 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

    51 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

    12 days ago

  • Add ">" in front of ids. sed -e 's/^/prefix/' file #Sed #Add #>

    Tags: Sed, Add

    301 days ago

  • To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta

    Tags: Sed, Clean, Header, Fasta

    278 days ago

  • Append the string to fasta header. $ sed 's/>.*/&_Bacteria/' foo.in > out.fasta #Sed #Fasta #String #Append

    Tags: Sed, Fasta, String, Append

    219 days ago

  • Remove four beginning characters from each line of the file. $ sed 's/^....//' genbank.txt #Remove #Sed #Text

    Tags: Remove, Sed, Text

    212 days ago