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Old 02-03-2010, 12:35 PM   #1
glacierbird
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Exclamation real world 454 sequencing data analysis examples?!

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?
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Old 02-03-2010, 12:50 PM   #2
glacierbird
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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.u...g.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.
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Old 02-06-2010, 05:25 AM   #3
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http://www.ncbi.nlm.nih.gov/sra/
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