Results for "Awk"
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Comment on "Run miniasm assembler on nanopore reads !"
...1 > ./minimap.paf.gz miniasm -f \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa awk ’/^S/{print “>...787 days ago
- ... awk [-off ...] [-F sep_re] [-v VA...p; Advanced feature filtering using awk syntax. &nbs...
1511 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ome/data/20170918_oly_pacbio_miniasm_reads.gfa 3 Convert miniasm output GFA to FASTA The FASTA file is needed to re-run minimap in Step 4 below. awk '$1 ~/S/ {print ">"$2"\n"$...2158 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...s.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$2"\n"$3}'...2166 days ago
Comment on "Perl one-liner for bioinformatician !!!"
Convert file to lowercase dd $ dd if=input.txt of=output.txt conv=lcase tr $ tr '[:upper:]' '[:lower:]' < input.txt > output.txt awk $ awk '{ print tolower($0) }' input.txt...2205 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Rename the name of multi fasta sequesnces with awk awk '/^>/{print ">chromosome" ++i; next}{print}' < file.fasta2971 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
One of the best known cheat sheet for AWKians www.catonmat.net/download/awk.cheat.sheet.txt3505 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
To deal with simple CSV: awk -F, '{print $1,$2}'3618 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
I love awk but recommend you to try bioawk . Bioawk is a modified version of awk which will parse some common sequence formats. https://github.com/lh3/bioawk3672 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Print line of a tab-delimited file when the 8th field is 10090:awk -F "\t" '$8 == 10090 { print $0 }' myFilePrint fields 1, 2, 3 from a tab-delimited file where the 4th field contains a '99':awk -F "\t" '$4 ~ /99/ {print $1"\t"$2"\t"$3}' myFile3700 days ago
