Exome sequencing analysis manual

[pc2009open]

This is a great document.

Thanks a lot. This is a great document. I wish I had read this document earlier.

[ulz_peter]

thanks for the hints. As we do not produce Illumina data in ourlab (yet) I haven't heard of those changes, although they seem to have been implemented a while ago...

the typo should mean following, I will rewrite that part and repost it...

[maubp]

You have a weird typo "foolwong" just above the FASTQ example.

Also your introduction about the different FASTQ encodings is out of date now. Illumina now follow the Sanger convention. They also changed the read naming convention, in particular the old /1 and /2 suffixes are gone

See this thread for details:

http://seqanswers.com/forums/showthread.php?t=8895

Also I've never heard FASTQ called a "FastAlignment and Quality file" (glossary on last page).

[liu_xt005]

Thanks a lot.

I have learned a lot.

[ulz_peter]

Hi Folks,

As I was writing a short guide of Exome analysis in our Institute, I thought it might be of some use to others especially for newbies, who need some kind of starting point to get to analysis of exome data (pretty much like the RNA-seq manual I once read in an older thread...). Instead of explaining everything in 100 new threads one could then point to that manual...

It is the way we do exome analysis at our Institute, but I would be happy if people help improve the manual, add their knowledge and expand it, like a common knowledge base for exome-level analysis.

I attached the pdf version and a .doc version within a zip folder, as the filesize was too large for uploading the doc file alone.

The most updated version can be found in the SeqWiki (http://seqanswers.com/wiki/How-to/exome_analysis)
(just to make it clear, it is not regularly updated and it's only goal is to get people started on the use of tools often used in exome sequencing)

Any comments highly appreciated!

P.S. I added a (very) short visualization chapter