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• • Jit@jit.aber

  

  awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

  2348 days ago

• • Jit@jit.aber

  

  #Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

  2348 days ago

• • BioJoker@biojoker

  

  Print the lqst line of the file zith Perl. $ perl -ne 'END {print $last} $last= $_ if /\S/' blocks_coords.gff #Last #Line #Perl

  1769 days ago

• • Jit@jit.aber

  

  samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam

  2308 days ago

• • Jit@jit.aber

  

  #GFA to #FASTA file conversion. awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

  2295 days ago

• • Jit@jit.aber

  

  #GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa

  2288 days ago

• • Rahul Nayak@rahul

  

  #Convert #fasta file to uppercase/lowercase, without altering the annotation line $ awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' name.fasta

  2249 days ago

• • Rahul Nayak@rahul

  

  #Split #multifasta $ cat hg18.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'

  2231 days ago

• • Manisha Mishra@manisha

  

  Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

  2224 days ago

• • Neelam Jha@neelam

  

  #Convert a #multi-line #fasta to a #singleline #fasta $ awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

  2168 days ago

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