Changes between Version 2 and Version 3 of BIOS_PreparedData


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Timestamp:
Sep 20, 2016 12:40:14 PM (13 months ago)
Author:
Rick
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  • BIOS_PreparedData

    v2 v3  
    44== Freeze I ==
    55=== Data available ===
    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 (see [wiki:BIOS_SampleBlacklist2 RNAseq 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.
     6Raw 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.
    77=== Location on VM ===
    88