2354 days ago
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Run bash script in Perl program !
...;my $in, 'command', 'arg1', 'arg2'); 5.a2p syntax: a2p [options] [awkscript] There is a Perl utility known as a2p which translates awk command to Perl. It takes awk...664 days ago
Linux command line exercises for NGS data processing
...torial [uzi@quince-srv2 ~/linuxTutorial]$ I have deliberately chosen Awk in the exercises as it is a l...line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to unders...2901 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
....fq reads.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}'...2378 days ago
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...3939 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...3806 days ago
3207 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2644 days ago
Download the genome from NCBI using bash script/command
...efseq/fungi/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...nk/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...seq/archaea/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...nvertebrate/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}...2559 days ago
3946 days ago
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 “>...823 days ago
1547 days ago