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

    3882 days ago

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

    Tags: Remove, line, sed, linux

    2573 days ago

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

    Tags: fasta, header, sed

    2445 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

    2308 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

    2268 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

    2107 days ago

  • sed -i 's/2019/2020/g' test.txt test2.txt test3.txt #Find #Replace #sed

    Tags: Find, Replace, sed

    732 days ago

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

    Tags: Sed, Add

    2558 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

    2534 days ago