wiki:BIOS_FirstPaper

Version 1 (modified by Rick, 13 months ago) (diff)

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First paper

The focus for our first paper are cell type-specific QTLs for transcription and mRNA processing.

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:

-- Table with number of samples per cohort and related statistics

(Some of this can already be found at this page, this page, this page, and on normalization.)

QTLs general:

Gene eQTLs:

Exon eQTLs:

Exon-ratio QTLs:

Poly(A) QTLs:

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

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.

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)
Gene eQTLs /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_23062014/
Transcript eQTLs /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_transcr_01062014/
Exon eQTLs /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_meta-exons_28062014/
Basophil-specific gene-level QTLs (FDR 0.05) /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_basophils_150714/
Eosinophil-specific gene-level QTLs (FDR 0.05) /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_eosinophils_150714/
Lymphocyte-specific gene-level QTLs (FDR 0.05) /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_lymphocytes_08062014/
Monocyte-specific gene-level QTLs (FDR 0.05) /virdir/Backup/dzhernakova/LL+RS+CODAM+LLS_eqtls_genes_monocytes_150714/
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
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
Basophil-specific exon-ratio QTLs (FDR 0.05) /virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-08-16
Eosinophil-specific exon-ratio QTLs (FDR 0.05) /virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-08-16
Lymphocyte-specific exon-ratio QTLs (FDR 0.05) /virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-08-16
Monocyte-specific exon-ratio QTLs (FDR 0.05) /virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-08-16
Neutrophil-specific exon-ratio QTLs (FDR 0.05) /virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-08-16
Basophil-specific exon-ratio QTLs (FDR 0.25) /virdir/Backup/RP3_data/exon-ratio-qtls/basophils-2014-09-03
Eosinophil-specific exon-ratio QTLs (FDR 0.25) /virdir/Backup/RP3_data/exon-ratio-qtls/eosinophils-2014-09-03
Lymphocyte-specific exon-ratio QTLs (FDR 0.25) /virdir/Backup/RP3_data/exon-ratio-qtls/lymphocytes-2014-09-03
Monocyte-specific exon-ratio QTLs (FDR 0.25) /virdir/Backup/RP3_data/exon-ratio-qtls/monocytes-2014-09-03
Neutrophil-specific exon-ratio QTLs (FDR 0.25) /virdir/Backup/RP3_data/exon-ratio-qtls/neutrophils-2014-09-03
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
Basophil-specific poly(A) QTLs (FDR 0.05) /virdir/Backup/RP3_data/polya-qtls/basophils-2014-08-18
Eosinophil-specific poly(A) QTLs (FDR 0.05) /virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-08-19
Lymphocyte-specific poly(A) QTLs (FDR 0.05) /virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-08-19
Monocyte-specific poly(A) QTLs (FDR 0.05) /virdir/Backup/RP3_data/polya-qtls/monocytes-2014-08-19
Neutrophil-specific poly(A) QTLs (FDR 0.05) /virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-08-19
Basophil-specific poly(A) QTLs (FDR 0.25) /virdir/Backup/RP3_data/polya-qtls/basophils-2014-09-04
Eosinophil-specific poly(A) QTLs (FDR 0.25) /virdir/Backup/RP3_data/polya-qtls/eosinophils-2014-09-04
Lymphocyte-specific poly(A) QTLs (FDR 0.25) /virdir/Backup/RP3_data/polya-qtls/lymphocytes-2014-09-04
Monocyte-specific poly(A) QTLs (FDR 0.25) /virdir/Backup/RP3_data/polya-qtls/monocytes-2014-09-04
Neutrophil-specific poly(A) QTLs (FDR 0.25) /virdir/Backup/RP3_data/polya-qtls/neutrophils-2014-09-04