Changes between Version 6 and Version 7 of BIOS_PreparedData
- Timestamp:
- Oct 19, 2016 10:47:41 AM (8 years ago)
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BIOS_PreparedData
v6 v7 1 1 = Recommended BIOS datasets for downstream analysis = 2 2 3 = = Freeze I ==4 = RNAseq data=3 = Freeze I = 4 == RNAseq data == 5 5 === Data available === 6 6 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. … … 19 19 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]] 20 20 21 = DNA methylation data=21 == DNA methylation data == 22 22 23 23 === Data available === … … 35 35 The Bioconductor/R packages minfi and illuminaio provide reading capabilities for the idat-files. 36 36 37 = Genotype data=37 == Genotype data == 38 38 39 39 === Data available === … … 55 55 Note that the HRC imputed data is in VCF format, which you may need to convert before usage. 56 56 57 = Phenotype data=57 == Phenotype data == 58 58 59 59 === Data available === … … 65 65 These files are available in .RData and .csv file formats. 66 66 See for column name explanations the page [wiki:BIOS_Phenotype Phenotype data]. Phenotype data is not complete yet: we are currently contacting the biobanks to complete there files. 67 67 68 === Location on VM === 68 69 … … 74 75 Link the files to the RNA-seq, genotype or methylation data by mapping the corresponding IDs. 75 76 76 = = Freeze II ==77 = Freeze II = 77 78 === Data available === 78 79 === Location on VM ===
