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. thanks Ad

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

On 10/05/2010 03:07 PM, Adrian Johnson 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. There's a brief overview at http://bioconductor.org/help/workflows/high-throughput-sequencing/ Also the updated biocViews widget at http://bioconductor.org/help/bioc-views/release/BiocViews.html e.g., Software / AssayTechnologies / HighThroughputSequencing Martin > > thanks > Ad > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793