real world 454 sequencing data analysis examples?!

[glacierbird]

Hi All,

I am interested in 454 data analysis, and plan to teach myself.

Could anybody kindly provides some data files and some potential problems that need to be solved, so that I can explore and find the solutions by myself.

Or any links to the tutorial with real examples?

[glacierbird]

ok, starting to collect info from this forum first:

# data

http://www.ebi.ac.uk/embl/Documentation/ENA-Reads.html

http://www.bioinformatics.bbsrc.ac.uk/training.html#seqmonk

# tips from "nickloman" & "mgogol"

1) Alignment to reference. Check out BWA, Bowtie, SSAHA2, SAMtools, VarScan and their respective papers. Cutting edge is probably Burrows-Wheeler Transform.

2) De novo assembly of short reads. Check out Velvet, SOAPdenovo. Cutting edge is probably de Bruijn graphs.

3) RNA-Seq. Usually one or both of the above methods combined with a counting software. Don't do much of this but you could start with Anthony Fejes' FindPeaks.

For RNA-seq data, you could look at:

tophat/cufflinks
fastx
R shortRead, DEGseq
genome browsers: UCSC with bigWig/BAM, IGV
Galaxy, BEDTools

I guess if you wanted to set yourself a project to try learning this stuff you could start by trying to find variations in genomes from the public 1,000 genomes project.

[glacierbird]

http://www.ncbi.nlm.nih.gov/sra/