Simulating reads with WGSim
Hello all, I'm new to SeqAnswers and I'm excited to contribute to the community. That being said, I was wondering if anyone has some tips for me. My goal is to learn how to simulate reads (such as from an Illumina) from a fasta file with a human reference chromosome information. This is what I have: the downloaded fasta files, SAMtools (haven't used them before though), WGSim (also have never used), and R. I have been trying to follow this tutorial http://biobits.org/samtools_primer.html but I seem to be stuck. First off, if I've downloaded Samtools do I need to 'build' it? I'm not sure what that means or where I enter the commands.I understand that once everything is in place this would be my first step, entering---> wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>. I assume I replace 'ref' from <in.ref.fa> with the filename for the reference chromosome (please correct me if I'm wrong). However, I can't figure out where to enter this command either. When I open WGSim it lists a long piece of code that I do not understand, and I don't see any command line. Any guidance would be greatly appreciated! 
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