Differences

This shows you the differences between two versions of the page.

--- data [2013/02/14 19:11]
wbiesing
+++ data [2014/08/10 20:57] (current)
ychen [DANN data]
@@ Line 1: / Line 1: @@
-====== Supplemental Data ======
+===== DANN data =====
-===== SREBP-1 ChIP-seq Data =====
-Included here is ChIP-Seq raw and processed data from:
+The raw data can be found here [[http://krishna.gs.washington.edu/martin/download/cadd_training/]]. The real SNV, insertion and deletion samples sum up to 16,627,775. We randomly sample equal number of simutation samples (SNV, insertion and deletion), combine with the real data, and get a dataset of 33,255,550 samples.
-//Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.//
+This dataset is transormed into svmlight format with script impute2svmlight.py, which is provided by Dr. Martin Kircher (the author of CADD paper), and the python package [[https://github.com/mblondel/svmlight-loader|svmlight-loader]]. We roughly partition the dataset into 80% for training, 10% for validation and 10% for testing. Their svmlight files are here:
-PNAS 2009 106:13765-13769; Young-Kyo Seo, Hansook Kim Chong, Aniello M. Infante, Seung-Soon Im, Xiaohui Xie, and Timothy F. Osborne
-  *  Raw sequence data (raw_data/*_sequence.txt) was processed using eland to create raw/*_eland_multi.txt
-  *  ChipSeq-mini 2.0 (http:<nowiki>//</nowiki>woldlab.caltech.edu/html/software, now part of the ERANGE package) was used to process the eland files and produce the processed/*.bed files.
-  *  IgG files are for the control run, SREBP1 files are after fasting and refeeding. See paper for details.
-  - [[http://cbclwiki.ics.uci.edu/public_data/SREBP1/processed/|Processed Data]]
-  - [[http://cbclwiki.ics.uci.edu/public_data/SREBP1/raw_data/|Raw Data]]
+===== tree-hmm sample .bam's from chr19 =====
-=====  FXR ChIP-seq Data =====
+tree-hmm sample data from the ENCODE human project [[http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data|http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data]]
-[[http://cbclwiki.ics.uci.edu/public_data/FXR/]]
+===== LRH-1 ChIP-seq Data =====
+Our ChIP-seq analysis of LRH-1 can be found at: [[http://cbcl.ics.uci.edu/public_data/LRH-1|http://cbcl.ics.uci.edu/public_data/LRH-1]]
+===== FXR ChIP-seq Data =====
+[[http://cbcl.ics.uci.edu/public_data/FXR/|http://cbcl.ics.uci.edu/public_data/FXR/]]
 ===== SREBP-2 ChIP-seq Data =====
-ChipSeq was performed on SREBP-2 and peaks were called using [[http://web.me.com/kaestnerlab1/GLITR/|GLITR]].  We also re-analyzed SREBP-1 using GLITR.
-Supplemental Tables, Figures, and datasets are available:
+ChipSeq was performed on SREBP-2 and peaks were called using [[http://web.me.com/kaestnerlab1/GLITR/|GLITR]].  We also re-analyzed SREBP-1 using GLITR. Supplemental Tables, Figures, and datasets are available: [[http://cbcl.ics.uci.edu/public_data/SREBP2/|SREBP2]]
-[[http://cbcl-1.ics.uci.edu/public_data/SREBP2/|SREBP2]]
+===== SREBP-1 ChIP-seq Data =====
+Included here is ChIP-Seq raw and processed data from:
+//Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.// PNAS 2009 106:13765-13769; Young-Kyo Seo, Hansook Kim Chong, Aniello M. Infante, Seung-Soon Im, Xiaohui Xie, and Timothy F. Osborne
+    * Raw sequence data (raw_data/%%*%%_sequence.txt) was processed using eland to create raw/%%*%%_eland_multi.txt
+    * ChipSeq-mini 2.0 (http:<nowiki>//</nowiki>woldlab.caltech.edu/html/software, now part of the ERANGE package) was used to process the eland files and produce the processed/%%*%%.bed files.
+    * IgG files are for the control run, SREBP1 files are after fasting and refeeding. See paper for details.
+    - [[http://cbcl.ics.uci.edu/public_data/SREBP1/processed/|Processed Data]]
+    - [[http://cbcl.ics.uci.edu/public_data/SREBP1/raw_data/|Raw Data]]