Changes between Version 5 and Version 6 of BIOS_PreparedData

Timestamp:

Oct 19, 2016 10:46:36 AM (8 years ago)

Author:

rick

Comment:

--

BIOS_PreparedData

@@ -1 +1 @@
 = Recommended BIOS datasets for downstream analysis =
 
+== Freeze I ==
 = RNAseq data =
-== Freeze I ==
 === Data available ===
 Raw RNA seq data is avalable at the grid, see [wiki:BIOS_RnaSeq RNASeq data]. This data has been aligned using the pipeline described at [wiki:BIOS_Pipeline RNAseq alignment and quantification pipeline], the exon, transcript and gene level count output is described in the following. Count data is available from the so called 'Freeze1': These are the 2116 samples from Groningen (N=626), Leiden (N=654), Rotterdam (N=652) and Maastricht (N=184) that passed QC. This is around half of the BIOS RNA seq data that is used for the first papers: the other half has been measured but is still in the process of aligning and QC. Both raw and TMM normalized data are available. TMM normalization corrects for the different library sizes across subjects, see attached script for R code or the R package edgeR, and http://genomebiology.com/2010/11/3/r25.
@@ -18 +18 @@
 Data is stored in R objects, by loading the files in R (e.g. type load('/virdir/Backup/RP3_data/RNASeq/run_01/exoncounts/exon_count_freeze1_R_object.RData') in R) there will be a matrix called RNA in your workspace for the raw data, and RNAs for the TMM normalized data. The row names of these matrices (type rownames(RNAs)) contain gene, exon or transcript IDs, the column names (colnames(RNAs) are the subject BIOS IDs (called uuid in other files). We used 
 ensembl v.71 for annotation, see [wiki:BIOS_ReferenceFiles Reference and annotation]. If you want to export the data to a tab delimited text file, use write.table(RNAs, file='yourfile.txt', quote =FALSE, col.names=TRUE, row.names=TRUE, sep='\t').[[BR]]
+
+= DNA methylation data =
 
 === Data available ===
@@ -76 +78 @@
 === Location on VM ===
 === How to use the data ===
-= DNA methylation data =