geuvadis_rna_analysis July 2012

geuvadis_rna_analysis@lists.crg.es

7 participants
14 discussions

[Geuvadis_rna_analysis] Analysis group TC July 26th

by Tuuli Lappalainen

Hello all, We're having a Geuvadis RNAseq analysis group call today (July 26th) at 2pm. Many people are on holidays, and we don't have a presentation scheduled for today, but let's have at least a short call to catch up on any analysis updates. After that we'll continue to discuss the QC companion paper. Call details are: from outside spain; 0034917911859 from spain; 900800678 Access code; 3160100 best regards, 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, 2 months

[Geuvadis_rna_analysis] mRNA sample information sheet

by Tuuli Lappalainen

Hello all, Here is a spreadsheet with information of which mRNA samples to use in analysis. Some numbers: - Total number of samples 667 with 464 unique individuals - 6 samples fail QC (QC_OK column == 0, with some description under QC_Info) - Total number of unique individuals that pass QC is 462 (UseThisSample==1) For individuals that have both the low-coverage and high-coverage replicate passing QC, I've always chosen the primary high-coverage sample. For the 5 replicates I took the one with the highest number of well mapped reads. I doubt that there will be a need to change the QC pass/fail status due to any future QC discoveries. However, we can add some other QC-related warnings in the QC_Info column of samples that pass QC. best regards, 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, 2 months

[Geuvadis_rna_analysis] Variant annotations

by Tuuli Lappalainen

Dear all, The functional annotations for all Geuvadis variants are now available. Many thanks to everyone in the loss-of-function group for all the work that it took to put this together. The file for all 1000g variants: /upload/geuvadis/wp4_rnaseq/main_project/external_data/genetic_variation/variant_info/ALL.phase1_release_v3.20101123.snps_indels_sv.sites.gdid.gdannot.v2.vcf.gz . The files of variants in Geuvadis data (genotype files and sites file) have also been updated to include the new annotations: /upload/geuvadis/wp4_rnaseq/main_project/external_data/genetic_variation/genotype/phase1_phase2/ The wiki is now read-only, so the documentation for this can be found in the following googledoc. https://docs.google.com/document/d/1wR0oyg01M-wfoWxjN7KX6c6UqqksbW_3to2_N7S… best regards, 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 I'll also upload the file to http://jungle.unige.ch/~lappalainen/ <http://jungle.unige.ch/%7Elappalainen/> The documentation is under the link below. Can you please take a look - especially Monkol and Manny - and let me know by Thursday if everything seems OK, and add/edit if necessary? I'll share this with the rest of the analysis group after that. https://docs.google.com/document/d/1wR0oyg01M-wfoWxjN7KX6c6UqqksbW_3to2_N7S… cheers, 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, 2 months

[Geuvadis_rna_analysis] quantification updates

by Tuuli Lappalainen

Hello all, The latest updates on the Geuvadis quantification data front: *Gene, exon and transcript quantifications *- the raw quantification data files of all 667 samples are available as before, unchanged - I changed the library depth normalization from what I uploaded a few days ago - please don't use the old files. - the normalized files now include only the 662 samples that we'll use in analysis *Intron and junction quantifications *- Micha's group has produced the quantifications: intron and junction read counts, and fractions of intron coverage - The available files are - raw gtf files, one per individual - tab-separated tables of the read counts and coverages: raw counts in 667 samples, and library depth normalized counts in 662 samples The directory is /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/ . See the readmes for details. A word about library depth normalization: before I normalized the exon quantifications by the total number of exonic reads. However, this is not a good correction for intronic reads, and for the sake of consistency I wanted to normalize exon, intron and junction quantifications by the same factor - thus, they are now all normalized by the total number of well mapped reads (mapped, properly paired, MAPQ>150, NM<=6). Have a nice weekend, 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, 3 months

[Geuvadis_rna_analysis] geuvadis samples to exclude

by Tuuli Lappalainen

Hello, Here is the final list of Geuvadis RNAseq samples to *exclude from all mRNA analyses:* NA18861.4.M_120208_5 (quantification, QC and ASE outlier) NA19225.6.M_120119_5 (ASE outlier probably due to contamination) HG00237.4.M_120208_1 (ASE outlier probably due to contamination) NA12399.7.M_120219_1 (ASE outlier probably due to contamination) NA07000.1.M_120209_2 (ASE outlier probably due to contamination) There are a couple of other samples to keep an eye on; within a couple of days I will finish the analysis of these and provide an updated sample information file with clear tags of samples to include in analysis and warning flags. best regards, 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, 3 months

[Geuvadis_rna_analysis] QC call on Thursday 26th at 3pm

by Tuuli Lappalainen

Dear all, We were planning with Peter to have a call to discuss the QC companion paper and QC analyses in general. We'll have the call on Thursday 26th at 3pm, i.e. right after our normal analysis group TC, and everyone who is interested is welcome to join. best regards, 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, 3 months

[Geuvadis_rna_analysis] RNAseq paper outline

by Tuuli Lappalainen

Hello all, I have drafted an outline for the Geuvadis RNAseq main paper based on the presentations and discussions at the Barcelona meeting. Please take a look and let me know if I've forgotten or misunderstood something, or if you have other suggestions. I will send it to the whole RNAseq group Friday afternoon, so I'd appreciate if you could send your comments before that. best regards, 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, 3 months

[Geuvadis_rna_analysis] No TC on July 19th

by Tuuli Lappalainen

Hello, Since we just had the Barcelona meeting, I suggest that we skip this week's Geuvadis analysis group call. But let's schedule one for next week, Thursday 26th of July. best regards, 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, 3 months

[Geuvadis_rna_analysis] geuvadis plotting colors

by Tuuli Lappalainen

Hello, In the Barcelona Geuvadis meeting I promised to send everyone a list of colors to use for populations and labs. They can be found below, please use these in all of your plots. best regards, Tuuli popnames <- c("CEU", "FIN", "GBR", "TSI", "YRI") Rpopcols <- c("red", "royalblue2", "olivedrab4", "purple1", "orange") The RGB values are as follows: Population R_color_name RGB_red RGB_green RGB_blue CEU red 255 0 0 FIN royalblue2 67 110 238 GBR olivedrab4 105 139 34 TSI purple1 155 48 255 YRI orange 255 165 0 labnumbers <- 1:7 labnames <- c("UNIGE", "CNAG_CRG", "MPIMG", "ICMB", "HMGU", "UU", "LUMC") Rlabcols <- c("mediumturquoise", "sienna3", "olivedrab4", "deeppink2", "purple1", "royalblue3", "darkgoldenrod1") SeqLabName SeqLabNumber R_color_name RGB_red RGB_green RGB_blue UNIGE 1 mediumturquoise 72 209 204 CNAG_CRG 2 sienna3 205 104 57 MPIMG 3 olivedrab4 105 139 34 ICMB 4 deeppink2 238 18 137 HMGU 5 purple1 155 48 255 UU 6 royalblue3 58 95 205 LUMC 7 darkgoldenrod1 255 185 15 -- 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, 3 months

[Geuvadis_rna_analysis] Splice junction and intron quantifications available

by Tuuli Lappalainen

Hello all, The final version of exon, gene and transcript quantifications are now on the ftp site in : /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/ . These are in Gencode v12 with the reads with >6 mismatches removed. See the readme files and wiki for documentation - there are both raw counts, counts normalized by the number of exonic reads, and RPKMs for transcripts. Note that the files include all 667 samples, and later this week I will send information of those samples provide files without the couple of samples that we'll drop from all analyses. Splice junction and intron quantifications will follow later this week. best regards, 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, 3 months

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geuvadis_rna_analysis July 2012