Results for "sed"

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  • Most Commonly used Awk by Bioinformatician

    ...practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call...input.txt deal with simple CSV: awk -F, '{print $1,$2}' substitution (sed is simpler in this case): aw...

    3875 days ago

  • Useful Publications and Websites for Deep Sequencing Data Analysis

    ...mapping and assembly of GC-biased genomes. Kozarewa et al, Natu...TileQC: a system for tile-based quality control of Solexa dat...of high-throughput sequence-based experimental data. Carver et...ipting Guide Tutorials for sed, the command-line stream edit...

    3742 days ago

  • Cheatsheet for Linux !!

    ...built from the updatedb command. Much faster than find    sed -i 's/day/night/g' file &mdas...le and replace them with night - s means substitude and g means global - sed also supports regular express...

    2836 days ago

  • Run miniasm assembler on nanopore reads !

    Miniasm is a very fast OLC-based de novo assembler for noisy long read...30000 AONTself.paf > AONTself30000.eps sed 's/_template_pass_FAH31515//'...20000 AONTself.paf > AONTself20000.eps sed 's/_template_pass_FAH31515//'...

    2292 days ago

  • Converting FASTQ to FASTA

    ...e methods are listed below. Using SED sed can be used to selective...sequence needed for fasta format. sed -n '1~4s/^@/>/p;2~4p' INFI...qret Standard script that can be used for many purposes. One such u...ote that you can use either compressed or uncompressed files for thi...

    2267 days ago

  • Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals

    ...ologist and bioinformatician to the frequently used tools for NGS analysis as wel...rom the updatedb command. Much faster than find sed -i 's/day/night/g' file ...night - s means substitude and g means global - sed also supports regular express...

    2243 days ago

  • Bioinformatics OneLiner

    ...e ends (\n) from a Unix text file: sed ':a;N;$!ba;s/\n//g' filename....To copy (move, rename, etc) files based on their list in a text file:...convert Illumina FASTQ 1.3 to 1.8: sed -e '4~4y/@ABCDEFGHIJKLMNOPQRS...0): grep "^>" scaffolds.fasta | sed s"/_/ /"g | awk '{ if ($4 >...

    2180 days ago