where can i get genome gc content

[dejavu2010]

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.

[id0]

-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.

[ECO]

Another vote for bedtools nuc.

[TheSeqGeek]

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

[TheSeqGeek]

solved!!

needed to make the fasta file into a single line

perlscrip called singleline.pl

#!/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

[Bioinform]

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

[Brian Bushnell]

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