Info on analyzing exome sequencing data

Tube-- · 11-09-2011, 07:19 AM

Hello! I'm a med student doing some research. I would need to analyze data, which came from exome analysis. I'm a real beginner with that. Do you guys know any good internet tutorials on exome sequencing in general and on analyzing the data that comes out of it? I mean real beginner things, I read the Wikipedia article on exome sequencing, it was way above my comprehension level. They don't really teach these thing on med school.

Thanks!

Heisman · 11-09-2011, 08:04 AM

You will probably like this thread: http://seqanswers.com/forums/showthr...uencing+manual

Tube-- · 11-15-2011, 03:52 AM

Thanks, I read briefly through it, but it seems that my data has already gone through those steps. I have an excel file that contains all the SNPs that were found. Now I should filter that SNP data somehow, to discover SNPs that are meaningful. The guys in the biotech lab used these tools:
SOLiD LifeScope software v. 2.1 (hg19)
Agilent Human hg19 all exon 50Mb kit target annotations

So now I have the SNP file in excel format that I should filter. Any ideas on how to start?

raonyguimaraes · 11-15-2011, 04:23 AM

GenoMax · 11-15-2011, 05:05 AM

Sounds like you want to map your SNP's to genes and go forward from there.

Look at this thread on biostar: http://biostar.stackexchange.com/que...ne-around-60kb

You can also use the BioMart tool in Ensembl (http://www.ensembl.org/Homo_sapiens/Info/Index) to do this (http://www.biomart.org/).

Depending on how many SNP's you have a simple search could be done this way: https://lists.soe.ucsc.edu/pipermail...ry/025082.html
You can also use the "table browser" from UCSC site to do lookups on multiple SNP's (http://genome.ucsc.edu/goldenPath/he...ablesHelp.html).

Quote:

Originally Posted by Tube--

Thanks, I read briefly through it, but it seems that my data has already gone through those steps. I have an excel file that contains all the SNPs that were found. Now I should filter that SNP data somehow, to discover SNPs that are meaningful. The guys in the biotech lab used these tools:
SOLiD LifeScope software v. 2.1 (hg19)
Agilent Human hg19 all exon 50Mb kit target annotations

So now I have the SNP file in excel format that I should filter. Any ideas on how to start?

spapillon · 11-30-2011, 08:41 AM

Tube--, it depends on the model of you disease and the data you have available. Are you looking at a recessive disease ? Is there consanguinity in the patients' family ? Is this a multiple patient cohort ? Do you have controls ? Are there any trios (father, mother, affected child) ?

As raonyguimaraes already showed, there are common steps one can use to filter out uninteresting SNPs. There are many ways to do so, raonyguimaraes show a pipeline that is commonly used. If you give us more details on the model of the disease and the actual data you have we'll be in a better standing to help you.

Simon

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Help finish the pipeline for human whole exome sequencing with paired reads data	wanguan2000	The Pipeline	1	07-31-2013 10:51 PM
PubMed: VarSifter: Visualizing and analyzing exome-scale sequence variation data on a	Newsbot!	Literature Watch	0	01-03-2012 02:00 AM
Bfast jobs for analyzing AB's SOLiD data vs Illumina data	genome_anawk1	Bioinformatics	1	08-24-2011 09:05 AM
Qs in exome sequencing data analysis	Maone	Genomic Resequencing	4	06-17-2011 07:32 AM
Maone, newbie in exome sequencing and data analysis	Maone	Introductions	0	06-15-2011 07:11 AM

11-09-2011, 07:19 AM	#1
Tube-- Junior Member Location: Finland Join Date: Nov 2011 Posts: 2	Info on analyzing exome sequencing data Hello! I'm a med student doing some research. I would need to analyze data, which came from exome analysis. I'm a real beginner with that. Do you guys know any good internet tutorials on exome sequencing in general and on analyzing the data that comes out of it? I mean real beginner things, I read the Wikipedia article on exome sequencing, it was way above my comprehension level. They don't really teach these thing on med school. Thanks!

11-09-2011, 08:04 AM	#2
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 534	You will probably like this thread: http://seqanswers.com/forums/showthr...uencing+manual

11-15-2011, 03:52 AM	#3
Tube-- Junior Member Location: Finland Join Date: Nov 2011 Posts: 2	Thanks, I read briefly through it, but it seems that my data has already gone through those steps. I have an excel file that contains all the SNPs that were found. Now I should filter that SNP data somehow, to discover SNPs that are meaningful. The guys in the biotech lab used these tools: SOLiD LifeScope software v. 2.1 (hg19) Agilent Human hg19 all exon 50Mb kit target annotations So now I have the SNP file in excel format that I should filter. Any ideas on how to start?

11-15-2011, 04:23 AM	#4
raonyguimaraes Member Location: Belo Horizonte - Brazil Join Date: Jun 2010 Posts: 38

11-30-2011, 08:41 AM	#6
spapillon Junior Member Location: Montreal, Canada Join Date: Nov 2011 Posts: 4	Tube--, it depends on the model of you disease and the data you have available. Are you looking at a recessive disease ? Is there consanguinity in the patients' family ? Is this a multiple patient cohort ? Do you have controls ? Are there any trios (father, mother, affected child) ? As raonyguimaraes already showed, there are common steps one can use to filter out uninteresting SNPs. There are many ways to do so, raonyguimaraes show a pipeline that is commonly used. If you give us more details on the model of the disease and the actual data you have we'll be in a better standing to help you. Simon