Human Body Map data?

steven · 10-27-2010, 08:42 AM

Hi,
do you know where to find data from illumina's human body map project?
I don't think there is anything publicly available, but just in case..
thanks,
s.

yinshe · 11-26-2010, 05:01 AM

They are incorporated in the IGV (Integrative Genomics Viewer).

bioinfosm · 11-27-2010, 11:59 AM

Quote:

Originally Posted by yinshe

They are incorporated in the IGV (Integrative Genomics Viewer).

Really! Do you have a link or resource to help explain that more?

yinshe · 11-28-2010, 07:53 AM

Here is the link:
http://www.broadinstitute.org/igv/

yinshe · 11-28-2010, 09:57 AM

Here is the link:

http://www.broadinstitute.org/igv/

The data is under hg18 genome.

bioinfosm · 11-29-2010, 10:18 AM

Quote:

Originally Posted by yinshe

They are incorporated in the IGV (Integrative Genomics Viewer).

All I could find is hosted genomes: http://www.broadinstitute.org/igv/Genomes

yinshe · 11-29-2010, 10:31 PM

I don´t know where is talking about this in the web page. Please try to install it in your computer and keep your computer online. Using human hg18 genome on the upper left. From "File", select "load from server", a new window will pop up. The last option is "Body Map 2.0".

steven · 11-30-2010, 08:15 AM

OK, i got it. Yinshe is right, you can download it from the IGV interface.

bioinfosm · 12-06-2010, 09:12 AM

Quote:

Originally Posted by yinshe

I don´t know where is talking about this in the web page. Please try to install it in your computer and keep your computer online. Using human hg18 genome on the upper left. From "File", select "load from server", a new window will pop up. The last option is "Body Map 2.0".

Oh thats what you meant. I can find it now. Thanks!

steven · 01-20-2011, 03:13 AM

It can also be downloaded without IGV:
/

-- update: not any more

Victory · 08-15-2011, 09:17 AM

Are there anyway we can download raw read or the raw alignment not the graphical one?

Jim Robinson · 08-16-2011, 06:26 AM

Hi, I think you might be able to get them from Ensemble. We (the IGV team) do not have permission to redistribute the BAM files. You could also ask Illumina.

Victory · 08-16-2011, 06:33 AM

thank you very much Jim.

steven · 08-16-2011, 09:45 AM

Quote:

Originally Posted by Jim Robinson

Hi, I think you might be able to get them from Ensemble. We (the IGV team) do not have permission to redistribute the BAM files. You could also ask Illumina.

Sorry Jim for having posted that information, I did not know I was not supposed to. I hope no harm was done.

Victory · 08-16-2011, 09:52 AM

I think it should be okay Steven. Your link is blocked for me and probably for others. I think you can remove that post to secure that no one can find the way to access it.

Jim Robinson · 08-16-2011, 12:00 PM

Hi Steven, no problem and no harm done, I disabled the link.

If anyone from Illumina is following this thread it would be a great service to the community if you could post instructions for obtaining the Body Map data, its a frequently asked question.

frozenlyse · 08-16-2011, 06:02 PM

The data has been put on GEO http://www.ncbi.nlm.nih.gov/projects...i?acc=GSE30611

JSF · 02-27-2013, 07:41 AM

You can also download all data (SRA, FastQ) here E-MTAB-513 http://www.ebi.ac.uk/arrayexpress/ex...nts/E-MTAB-513

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10-27-2010, 08:42 AM	#1
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	Human Body Map data? Hi, do you know where to find data from illumina's human body map project? I don't think there is anything publicly available, but just in case.. thanks, s.

01-20-2011, 03:13 AM	#10
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	It can also be downloaded without IGV: / -- update: not any more Last edited by steven; 08-16-2011 at 09:56 AM. Reason: That url should not be disclosed

11-26-2010, 05:01 AM	#2
yinshe Member Location: Norway Join Date: Oct 2010 Posts: 20	They are incorporated in the IGV (Integrative Genomics Viewer).

11-28-2010, 07:53 AM	#4
yinshe Member Location: Norway Join Date: Oct 2010 Posts: 20	Here is the link: http://www.broadinstitute.org/igv/

11-28-2010, 09:57 AM	#5
yinshe Member Location: Norway Join Date: Oct 2010 Posts: 20	Here is the link: http://www.broadinstitute.org/igv/ The data is under hg18 genome.

11-29-2010, 10:31 PM	#7
yinshe Member Location: Norway Join Date: Oct 2010 Posts: 20	I don´t know where is talking about this in the web page. Please try to install it in your computer and keep your computer online. Using human hg18 genome on the upper left. From "File", select "load from server", a new window will pop up. The last option is "Body Map 2.0".

11-30-2010, 08:15 AM	#8
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	OK, i got it. Yinshe is right, you can download it from the IGV interface.

08-15-2011, 09:17 AM	#11
Victory Member Location: Pennsylvania Join Date: Nov 2009 Posts: 13	Are there anyway we can download raw read or the raw alignment not the graphical one?

08-16-2011, 06:26 AM	#12
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi, I think you might be able to get them from Ensemble. We (the IGV team) do not have permission to redistribute the BAM files. You could also ask Illumina.

08-16-2011, 06:33 AM	#13
Victory Member Location: Pennsylvania Join Date: Nov 2009 Posts: 13	thank you very much Jim.

08-16-2011, 09:52 AM	#15
Victory Member Location: Pennsylvania Join Date: Nov 2009 Posts: 13	I think it should be okay Steven. Your link is blocked for me and probably for others. I think you can remove that post to secure that no one can find the way to access it.

08-16-2011, 12:00 PM	#16
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi Steven, no problem and no harm done, I disabled the link. If anyone from Illumina is following this thread it would be a great service to the community if you could post instructions for obtaining the Body Map data, its a frequently asked question.

08-16-2011, 06:02 PM	#17
frozenlyse Senior Member Location: Australia Join Date: Sep 2008 Posts: 136	The data has been put on GEO http://www.ncbi.nlm.nih.gov/projects...i?acc=GSE30611

02-27-2013, 07:41 AM	#18
JSF Junior Member Location: MO Join Date: Jan 2013 Posts: 1	You can also download all data (SRA, FastQ) here E-MTAB-513 http://www.ebi.ac.uk/arrayexpress/ex...nts/E-MTAB-513