Database of tumor-normal reads

desmo · 12-14-2011, 07:17 AM

Hi everybody,
I've just started to work on cancer genomic (using ngs) and I would like to test some tools. Unfortunately right now I don't have any available reads.
Anyone knows where I can find some tumor-normal reads.
Thanks in advance.

adaptivegenome · 12-14-2011, 07:19 AM

Look up TCGA...

GenePool · 03-27-2014, 11:21 AM

Hi All,

We've included TCGA gene-level read counts as part of freely available reference library of genomics data in our product, GenePool. These counts were generated using the RNASeqV2 pipeline that leveraged RSEM. We've also taken the time to extract and curate the sample-level metadata and make it easily available to researchers to subset the samples, and analyze the data accordingly. For more advanced users, you can easily just export out the read counts and sample level metadata and get into more high-powered statistical analyses.

Incidentally, we've also included the isoform-, splice junction-, and exon-level counts into GenePool's premium content.

If you're interested in learning more, please check out GenePool's growing genomics library, check out the following threads:

http://seqanswers.com/forums/showthread.php?t=42471
http://seqanswers.com/forums/showthread.php?t=48485

We'd love to have your feedback on this effort.

------------------------------
GenePool is making genomics data management, analysis, and sharing easier!
Products @ www.stationxinc.com

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12-14-2011, 07:17 AM	#1
desmo Member Location: Pavia Join Date: Nov 2011 Posts: 25	Database of tumor-normal reads Hi everybody, I've just started to work on cancer genomic (using ngs) and I would like to test some tools. Unfortunately right now I don't have any available reads. Anyone knows where I can find some tumor-normal reads. Thanks in advance.

03-27-2014, 11:21 AM	#3
GenePool Registered Vendor Location: San Francisco, CA Join Date: Mar 2014 Posts: 18	Hi All, We've included TCGA gene-level read counts as part of freely available reference library of genomics data in our product, GenePool. These counts were generated using the RNASeqV2 pipeline that leveraged RSEM. We've also taken the time to extract and curate the sample-level metadata and make it easily available to researchers to subset the samples, and analyze the data accordingly. For more advanced users, you can easily just export out the read counts and sample level metadata and get into more high-powered statistical analyses. Incidentally, we've also included the isoform-, splice junction-, and exon-level counts into GenePool's premium content. If you're interested in learning more, please check out GenePool's growing genomics library, check out the following threads: http://seqanswers.com/forums/showthread.php?t=42471 http://seqanswers.com/forums/showthread.php?t=48485 We'd love to have your feedback on this effort. ------------------------------ GenePool is making genomics data management, analysis, and sharing easier! Products @ www.stationxinc.com Last edited by GenePool; 11-23-2014 at 10:01 PM.

12-14-2011, 07:19 AM	#2
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	Look up TCGA...