Sequencing beginner looking for review articles

[johnadam33]

Hi there,
I am new to sequencing. I have absolutely no idea what I get from the sequencing and how I proceed further. I know it sounds crazy. I am very interested in sequencing and bioinformatics and that's the reason for me moving to this field from conventional methods.
Is there any paper or website that talks in detail what it is and what are the steps one should follow once u get the sequence back and also the analysis part. I am working on SOLiD platform, doing exome sequencing.

I really appreciate it if you all can help me find a source to get started such as a paper or book or website.

Info I am looking at it is the steps in the process...such as get the data and then check the quality, align and find mutations and son on....

Thanks,
John.

[johnadam33]

Any productive suggestion will be appreciated...

[dp05yk]

Here may be a decent paper:

http://www.ncbi.nlm.nih.gov/pubmed/19997069

[johnadam33]

Dp0 5yk,
Thanks for the link , but that paper talks about the platforms and nothing about data analysis...anything for data analysis?
Thanks.

[GW_OK]

http://www.broadinstitute.org/gsa/wi....php/Main_Page

That's the GATK suite website, it's pretty in depth and you can get some sense of what analysis needs to be done even if you don't use those programs.

[johnadam33]

GW_OK,Thanks a lot. That was helpful. I will get back to you if I need more help.

[johnadam33]

I can't believe there is not even a single paper or website that explains how nextgen sequencing works, other than going on and on about platforms and their applications. I don't know why not even a single author thought about writing about it. Weird...everyone now a days talks about NGS, but no one knows how it is done...unless u pay lot of money to sit thru a workshop.

[GW_OK]

There's plenty of articles talking about how it works. This one, for example:

Ansorge WJ.
Next-generation DNA sequencing techniques.
N Biotechnol. 2009 Apr;25(4):195-203. Epub 2009 Feb 3.

has a nice overview. Now, as far as what to do with all the data, lots of people do lots of different things so there's no set in stone methodology as of yet. Some precedents are being set for certain types of projects, like exomes/whole genomes, whereby people are mostly following what the larger centers are doing.

Science isn't always cut and dried, unless you're working in a more well-traveled discipline. When you're doing things no one else has done, you have to kinda make it up as you go along.

[ECO]

Moving to general. OP, please try searching either here or PubMed as there are many reviews discussing all aspects of what you are interested in.

[johnadam33]

Thanks GW_OK and ECO. That was helpful. Now, is there any other book or paper that talks about steps involved in proceeding iwth the data? Once u get the data from machine, what are the steps one should follow such as image conversions and bam and sam tools and all those other things....

[protist]

Some nice reviews are:

Computational methods for transcriptome annotation and quantification using RNA-seq.
Garber M, Grabherr MG, Guttman M, Trapnell C.
Nat Methods. 2011 Jun;8(6):469-77. Epub 2011 May 27.

How to map billions of short reads onto genomes.
Trapnell C, Salzberg SL.
Nat Biotechnol. 2009 May;27(5):455-7.

Computation for ChIP-seq and RNA-seq studies.
Pepke S, Wold B, Mortazavi A.
Nat Methods. 2009 Nov;6(11 Suppl):S22-32.

[samanta]

Hi there,
I am new to sequencing. I have absolutely no idea what I get from the sequencing and how I proceed further. I know it sounds crazy. I am very interested in sequencing and bioinformatics and that's the reason for me moving to this field from conventional methods.
Is there any paper or website that talks in detail what it is and what are the steps one should follow once u get the sequence back and also the analysis part. I am working on SOLiD platform, doing exome sequencing.

I really appreciate it if you all can help me find a source to get started such as a paper or book or website.

Info I am looking at it is the steps in the process...such as get the data and then check the quality, align and find mutations and son on....

Thanks,
John.

You may try my blog here - http://homolog.us/blogs. It is not published paper, but we covered everything from SOLiD platform to bioinformatics to how the NGS sequences are assembled.

Best !