[BioC] help - where to start

[Steve Lianoglou]

On Tue, Oct 5, 2010 at 6:07 PM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
> Hello group,
> I just have my fastq files from a sequencing group. what kind of
> diagnostics one can do using bioconductor? I have a slight idea about
> ngs but do not know where to start?
> What kind of quality assessment tools can be applied on fastq files to
> find if the quality of the reads are good.
> Sorry for a very naive question, just taking baby steps.

* you could plot average phred score @ each base position
* you could look for (unexpected) sequence biases ...
* ...

But honestly, before you begin you should really first read some
review/overviews of NGS protocols so you can do some informed analysis
(if I recall there were a few in Nature(something) around the end of
last year, start of this year(?))

That having been said, if you're just working on a fastq file and want
to stay in the bioconductor realm, have a look at the ShortRead
package:

http://www.bioconductor.org/help/bioc-views/release/bioc/html/ShortRead.html

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact