geuvadis_rna_analysis September 2012

geuvadis_rna_analysis@lists.crg.es

9 participants
13 discussions

by Tuuli Emilia LAPPALAINEN

Hello, Let's skip tomorrow's Geuvadis analysis group teleconference since there is no presentation scheduled, and it's a public holiday in Geneva. The next one will be on the 13th. best regards, Tuuli

12 years, 1 month

[Geuvadis_rna_analysis] ASE results fixed

by Tuuli Emilia LAPPALAINEN

Dear all, I found a small bug in the ASE results - nothing major, but for any final analysis please use the new file that I uploaded today to the same place as before: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/ase . Apologies for any extra work that this may have caused. best, Tuuli

12 years, 1 month

[Geuvadis_rna_analysis] important: sample QC updates

by Tuuli Lappalainen

Hello all, IMPORTANT: - sample NA19095.5.M_120131_5 should be excluded from all analyses. This sample is one of the 5 replicates, and for this individual we originally chose another sample (NA19095.2.M_120131_2) to use. Thus, the set of unique 462 samples (which should be used in most analyses) doesn't change. However, if you're analyzing replicates in any way, exclude NA19095.5.M_120131_5. Some more info: Peter did analysis of sex-specific expression, which generally shows very nice clustering to female and male samples. However, 4 samples showed a mixed pattern that is suggestive of cross-contamination. Three of these have been excluded previously due to them showing clear signs of contamination in ASE analysis ( NA12399.7.M_120219_1, NA07000.1.M_120209_2, HG00237.4.M_120208_1). However, the sample NA19095.5.M_120131_5 behaved slightly abnormally in ASE analysis but was not excluded based on that, but the sex-specific analysis shows that this sample needs to be thrown out. Additionally, there are some QC warnings for samples that will be kept in the dataset. In the sex-specific transcription analysis the sample NA11930.3.M_120202_8 behaved slightly abnormally, and Jonas and Olof have also listed samples that are slight outliers based on different statistics. An updated sample information sheet is in the attachment. The UseThisSample flag gives you the set of 462 unique samples (and hasn't changed from the previous file (GD667_mRNA_SampleInformation_270712.txt). Additionally, the QC_OK column denotes all the samples that have passed QC, and QC_Info has information of why a sample failed QC, or QC warnings for QC-passed samples, and these two columns have been updated with the information above. This information can be found in the wiki (http://sanabre.net/geuvadis/index.php/QC_sample_info), and the sample information sheets have been uploaded on the ftp site (/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc) best, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

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geuvadis_rna_analysis September 2012