Hi,

I would like to know how complex it is to analyze NGS Data. Is it possible to learn NGS data analysis from the online resources or should we learn under the guidance of an expert? How to get the core concepts of NGS data analysis? How to configure parameters while using open source tools? (Assembly, Alignment, statistics etc ). I have a masters degree in bioinformatics with unix, perl and basic core Java skills. Any advice is appreciated.
<ul>
<li>download <a href='http://bio-bwa.sourceforge.net/'>bwa</a>, <a href='http://samtools.sourceforge.net/'>samtools</a> and a reference genome.</li>
<li>generate a random set of reads using <a href='http://samtools.sourceforge.net/'>samtools</a>/misc/wgsim</li>
<li>index the genome</li>
<li>align the reads  and generate a <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> output.</li>
<li>describe each column of the <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a></li>
<li>generate a vcf from the <a href='http://samtools.sourceforge.net/SAM1.pdf'>sam</a> using <a href='http://samtools.sourceforge.net/'>samtools</a>/mpileup</li>
<li>describe each column of the vcf</li>
<li>use ensembl/vep to predict the consequences of the variations.</li>
</ul>
