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  • where can i get genome gc content

    I am trying to use RNA-SeQC for a mouse rnaseq dataset. the program requires mouse gc content file. Where can i download it or how can i generate it by myself? Thanks a lot.

  • #2
    Code:
    -gc <arg>     File of transcript id <tab> gc content. Used for stratification
    Technically, it's not required, but if you want to use it, you convert your GTF/GFF file to BED format by cutting the proper columns. Then use "bedtools nuc" to get GC content for each region.

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    • #3
      Another vote for bedtools nuc.

      Comment


      • #4
        Originally posted by ECO View Post
        Another vote for bedtools nuc.
        So i ran this an I got the wrong counts

        The numbers are just off... the start and stop bases match everything looks good but the % is off...

        A + G + T + C = correct lengths per gene but the #A + #G + #T + #C are different from what it should be..


        What's up with that?

        129-79-59-15:bin User$ ./bedtools nuc -fi genome.fasta -bed chromosome.gff > gcconent

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        • #5
          solved!!

          needed to make the fasta file into a single line

          perlscrip called singleline.pl

          Code:
          #!/usr/bin/perl -w
          #perl fa2oneline.pl sample.fa > out.fa
          # downloaded from http://www.bioinformatics-made-simple.com
          # change multiline fasta to single line fasta
          use strict;
          
          my $input_fasta=$ARGV[0];
          open(IN,"<$input_fasta") || die ("Error opening $input_fasta $!");
          
          my $line = <IN>; 
          print $line;
          
          while ($line = <IN>)
          {
          chomp $line;
          if ($line=~m/^>/) { print "\n",$line,"\n"; }
          else { print $line; }
          }
          
          print "\n";
          perl singleline.pl input.fasta > output.fasta

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          • #6
            Hi i am new to perl, i want to get GC content from a whole genome with sliding window size of say 10000bp what changes should i make in the above script.


            thanks
            Bioinform

            Comment


            • #7
              The GC content of a genome is unrelated to sliding window size.

              You can run the stats.sh script to get the GC content of a genome. e.g.

              stats.sh genome.fasta

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