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• • Jit@jit.aber

  

  Remove tab with comma in file: perl -lpe 's/\t/,/g' < flattened_line_0.fa.data > output.csv #PerlTrick #PerlO,liner #Perl #Tab #Comma

  2847 days ago

• • Hardeep Kaur@hardeep

  

  Genome and coverage https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf #Coverage #Genome #Depth #Reads #NGS

  2737 days ago

• • Jit@jit.aber

  

  Find a file with certain size and delete them: $ find . -name "see-D-d-ALN_*" -size -10k -delete #Delete #Size #Linux #Tricks

  2814 days ago

• • Radha Agarkar@radhaagarkar

  

  Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta

  2803 days ago

• • Radha Agarkar@radhaagarkar

  

  Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file #PerlTricks #PerlOneliner #Perl #Extract #Ids #

  2803 days ago

• • Jit@jit.aber

  

  Split the text file with line number in Linux: wc -l abc.txt and then: split -l 60000 abc.txt #Split #Break #Line #Ubuntu #Linux #Tricks

  2796 days ago

• • Shruti Paniwala@shruti

  

  Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

  2763 days ago

• • Jit@jit.aber

  

  Accept file from STDIN in Perl my $infh = \*STDIN; my $outfh = \*STDOUT #Perl #Tricks

  2712 days ago

• • Jit@jit.aber

  

  Understanding and manipulating SAM/BAM alignment files http://homer.salk.edu/homer/basicTutorial/samfiles.html #SAM #BAM #File #Explain

  2642 days ago

• • Shruti Paniwala@shruti

  

  Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

  2674 days ago

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