= First paper = The focus for our first paper are cell type-specific QTLs for transcription and mRNA processing. [https://docs.google.com/document/d/1HoLmhJD0L2nmPF8Xr9jotm-wF1h7UWPj35YCug0tio4/edit Outline and division of work (2014-05-21)] == Todo list == - todo == Figures and Tables == Please create one subpage `FgFirstPaper/FigureName` per figure/table and put the underlying data there and an example plot. It will then be easy to make a polished set of plots from the underlying data. '''Data and QC:''' -- [wiki:FgFirstPaper/table_with_number_of_samples_per_cohort_and_related_statistics Table with number of samples per cohort and related statistics] [[BR]] - [wiki:FgFirstPaper/table_with_general_sequencing_characteristics Table with general sequencing characteristics: average and range for][[BR]] -- [wiki:FgFirstPaper/qc_and_alignment_stats number of reads passing qc][[BR]] -- [wiki:FgFirstPaper/qc_and_alignment_stats number (percentage) of aligned reads][[BR]] -- [wiki:FgFirstPaper/qc_and_alignment_stats number (percentage) of aligned reads mapping to our annotated exons][[BR]] -- number of detected genes (>0 count) per sample[[BR]] - Graphs with:[[BR]] -- [wiki:FgFirstPaper/gc_distribution_per_biobank GC distribution per biobank][[BR]] -- [wiki:FgFirstPaper/RNA_blood_sampling_age_distribution_per_biobank_plot RNA blood sampling age distribution per biobank][[BR]] -- [wiki:FgFirstPaper/genotype_concordance_plots Genotype concordance per biobank][[BR]] -- [wiki:FgFirstPaper/genotype_concordance_plots Heterozygosity per biobank] [[BR]] - Density plot of median Spearman correlations for genes and exons (Peter-Bram)[[BR]] - MDS plot of Spearman correlations colored by GC such as [raw-attachment:mdsplot_exon_filt_colored_gc.pdf:wiki:FgGeneExonTranscriptCounts this one] (Peter-Bram)[[BR]] - [wiki:FgFirstPaper/PCs_phenotypes_correlations Significant correlations between PCs and sample characteristics] [[BR]] (Some of this can already be found at [wiki:FgGeneExonTranscriptCounts this page], [wiki:FgPrimeBias this page], [wiki:FgQualityControl/FgQualityControlRun1 this page], and on normalization.) '''QTLs general:''' - [wiki:FgQTL/cis/QTL_numbers The summary statistics table with the number of QTLs] - [raw-attachment:run1_eQTLs_numbers.xlsx:wiki:FgQTL/cis/gene-eQTL Table of the number of primary/secondary/tertiary effects]. Details can be found on [wiki:FgQTL/cis/gene-eQTL this] page - [wiki:FgFirstPaper/histogram_numCisEffects Histogram of genes with x independent QTLs] - [wiki:FgFirstPaper/histogram_numCisEffects_exons Histogram of exons with x independent QTLs] - [wiki:FgFirstPaper/venn_eQTL_overlap Venn diagram of gene-, transcript-, exon-level eQTLs overlap] - Replication results for GEUVADIS of [wiki:FgQTL/cis/gene-eQTL gene level eQTLs] and [wiki:FgQTL/cis/exon-eQTL exon level eQTLs] - Replication in Array data ([wiki:FgQTL/cis/gene-eQTL Westra et al], Wright et al (NTR+NESDA data)) (Dasha) - [wiki:FgFirstPaper/EffectLevels Number of independent cis-effects after stepwise regression] - [wiki:FgFirstPaper/QTLDistanceToExon Distance to exon midpoint of top SNPs for exon/exon-ratio/polya QTLs] '''Gene eQTLs:''' - [wiki:FgFirstPaper/geneEqtls_distanceToTSS distance top SNP relative to transcription start site] - [wiki:FgFirstPaper/geneEqtls_distanceToTES distance top SNP relative to transcription end site] - [raw-attachment:run1_eQTLs_numbers.xlsx:wiki:FgQTL/celltype Table of the number of cell-type specific effects]. Details can be found on [wiki:FgQTL/celltype this] page - [wiki:FgFirstPaper/Enriched_TF_Binding_Sites Top 10 TF binding sites enriched in global eQTL SNPs (Maarten)][[BR]] - Top SNPs show a change in affinity for specific TF (Szymon) - Interaction analysis (TF expression levels modify eQTL effect) overlapped with enriched TFs (Dasha and Maarten/Szymon) '''Exon eQTLs:''' - [wiki:FgFirstPaper/exonEqtls_distanceToMidExon distance top SNP relative to exon mid point] '''Exon-ratio QTLs:''' - [wiki:FgFirstPaper/ExonRatioQTLDistanceToExon Distance of (top) SNP relative to exon start] - [wiki:FgFirstPaper/ExonRatioExonClassification Classification of exons with exon-ratio QTLs (constitutive, cassette etc.)] - [wiki:FgFirstPaper/ExonRatioAcceptorDonorOverlap Overlap of QTL SNPs with donor/acceptor sites] - Enrichment of RNA-binding protein motifs ([wiki:FgQTL/exon-ratio/motifs preliminary analysis]) - Example gene(s) (after overlapping with GWAS hits?) '''Poly(A) QTLs:''' - [wiki:FgFirstPaper/PolyAQTLDistanceToSite Distance of (top) SNP relative to polyadenylation site] - Overlap / enrichment of top SNP per poly(A) site with canonical and alternative poly(A) signals (Martijn) - Example gene(s) (after overlapping with GWAS hits?) '''Cell type-specific eQTLs and exon-ratio QTLs''' - Table with number of Cell type-specific results for FDR 0.05 and 0.25 (Gene and exon ratio) - TF binding and RNA binding protein analyses for cell-type specific eQTLs == Materials & Methods == [https://docs.google.com/document/d/1l1livkojjX2ajbTxaotQO0DoSxZ31xR3XfXVzqQPJuI/edit Google Docs] == Scripts and pipelines to deposit == Many things could (or already are) be deposited in !GitHub or !GitLab. It would be nice to have a page with a general overview of all scripts and pipelines. - [https://git.lumc.nl/groups/rp3 RP3 on GitLab] - [https://github.com/molgenis/systemsgenetics/tree/master/eqtl-mapping-pipeline QTL mapping pipeline] == Data to deposit == To be decided: - Where to deposit? Molgenis site is nice for downstream results and browsing. Probably not for raw sequencing data. - Primary data: fastq files, BAM files? - Secondary data: expression/count files? Cell counts? - For all QTL findings, what to deposit: all QTLs, only significant findings, or only the top hit per gene? All data, or just the SNP-probe pairs? ||= Data =||= Location (on VM unless noted otherwise) =|| || [wiki:FgQTL/cis/gene-eQTL Gene eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_23062014/` || || [wiki:FgQTL/cis/transcript-eQTL Transcript eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_transcr_01062014/` || || [wiki:FgQTL/cis/exon-eQTL Exon eQTLs] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_meta-exons_28062014/` || || [wiki:FgQTL/celltype Basophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_150714/` || || [wiki:FgQTL/celltype Eosinophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_150714/` || || [wiki:FgQTL/celltype Lymphocyte-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_08062014/` || || [wiki:FgQTL/celltype Monocyte-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_150714/` || || [wiki:FgQTL/celltype Neutrophil-specific gene-level QTLs (FDR 0.05)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_150714/` || || [Basophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_fdr0.25_05082014` || || [Eosinophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_fdr0.25_05082014` || || [Lymphocyte-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_fdr0.25_05082014` || || [Monocyte-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_fdr0.25_05082014` || || [Neutrophil-specific gene-level QTLs (FDR 0.25)] || `/virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_neutrophils_fdr0.25_05082014` || || [wiki:FgQTL/exon-ratio#a2014-07-23exonratioQTLs Exon-ratio QTLs] || `/virdir/Backup/RP3_data/exon-ratio-qtls/2014-07-23` || || Exon-ratio QTLs (secondary effects) || `/virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-secondary-2014-09-10` || || Exon-ratio QTLs (tertiary effects) || `/virdir/Backup/RP3_data/exon-ratio-qtls/snps-present-in-all-datasets-tertiary-2014-09-10` || || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Basophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-08-16` || || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Eosinophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-08-16` || || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Lymphocyte-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-08-16` || || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Monocyte-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-08-16` || || [wiki:FgQTL/exon-ratio#a2014-08-16celltypespecificexonratioQTLs Neutrophil-specific exon-ratio QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-08-16` || || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Basophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-09-03` || || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Eosinophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-09-03` || || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Lymphocyte-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-09-03` || || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Monocyte-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-09-03` || || [wiki:FgQTL/exon-ratio#a2014-09-03celltypespecificexonratioQTLs Neutrophil-specific exon-ratio QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-09-03` || || [wiki:FgQTL/apa#a2014-06-20polyaQTLs250kbwindow Poly(A) QTLs] || `/virdir/Backup/RP3_data/polya-qtls/2014-06-20` || || Poly(A) QTLs (secondary effects) || `/virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-secondary-2014-09-29` || || Poly(A) QTLs (tertiary effects) || `/virdir/Backup/RP3_data/polya-qtls/snps-present-in-all-datasets-tertiary-2014-09-30` || || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Basophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/basophils-2014-08-18` || || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Eosinophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-08-19` || || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Lymphocyte-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-08-19` || || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Monocyte-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/monocytes-2014-08-19` || || [wiki:FgQTL/apa#a2014-08-19celltypespecificpolyaQTLs250kbwindow Neutrophil-specific poly(A) QTLs (FDR 0.05)] || `/virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-08-19` || || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Basophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/basophils-2014-09-04` || || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Eosinophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-09-04` || || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Lymphocyte-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-09-04` || || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Monocyte-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/monocytes-2014-09-04` || || [wiki:FgQTL/apa#a2014-09-04celltypespecificpolyaQTLs250kbwindow Neutrophil-specific poly(A) QTLs (FDR 0.25)] || `/virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-09-04` ||