Results for "Awk"
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Most Commonly used Awk by Bioinformatician
...its functionality with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline o...thing on the fly. You can use awk to make a neat one-liner for...}' input.txt > output.txt awk 'BEGIN{OFS="\t"}{print $2,$4,...ed is simpler in this case): awk '{sub(/test/, "no", $0);print...3902 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...BMC Bioinformatics 11(Suppl 12):S1, 2010 Full Text Links to Linux command-line tutorials and resources Tutorials for AWK, a powerful tool for handling data tables A set of awk notes from Boston University...3769 days ago
Run miniasm assembler on nanopore reads !
...ava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf awk '{if($1==$6){print}}' AONT.paf > AONTself.paf awk '$5=="-"' AONTself.paf | awk..._A.fasta AONT.paf > AONT.gfa grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' >...2320 days ago
- ...rsion seqret -sequence reads.fastq -outseq reads.fasta awk can be used for conversion as follows: Using AWK cat infile.fq | awk '{if(NR%...[-o OUTFILE] = FASTA output file. default is STDOUT. Bioawk Another option to convert fa...
2295 days ago
Awk for Bioinformatician and computational biologist
Awk is a programming language whi...ions}' file The working of Awk is as followsAwk reads the in...ch pattern is not given, then Awk performs the given actions fo...atches the pattern contig3 $ awk '/contig3/' data/test.tsvcont...nces with lengths > 14: $ awk '{print (length($2)>14) ?...2270 days ago
- ...l sequences in a fasta file: awk '/^>/ {if (seqlen){print s...ne copy of duplicated lines: awk '!seen[$0]++' To sum assembl...file into many fasta files: awk '/^>/ {OUT=substr($0,2) "....a headers from a fasta file. awk '/^>/{f=!d[$1];d[$1]=1}f'...
2207 days ago
