Peptide analysis

CSD3 directory

/rds/project/jmmh2/rds-jmmh2-projects/Caprion_proteomics/analysis/

Scripts and results

The project directory above contains scripts at peptide_progs/ and results results at peptide/, respectively.

Script name Description Protein-specific error/output
0_utils.sh Code snippets
1_pgwas.sh Association analysis1 {protein}.e / {protein}.o
2_meta_analysis.sh Meta-analysis {protein}-METAL_{SLURM_job_id}_{phenotype_number}.e / {protein}-METAL_{SLURM_job_id}_{phenotype_number}.o
3 Signal identification2
3.1_extract.sh Signal extraction _step1_{SLURM_job_id}_{phenotype_number}.e / _step1_{SLURM_job_id}_{phenotype_number}.o
3.2_collect.sh Signal collection/classification _step2_{protein}.e / _step2_{protein}.o
3.3_plot.sh Forest, Q-Q, Manhattan, LocusZoom, mean-by-genotype/dosage plots _step3_{SLURM_job_id}_{phenotype_number}.e / _step3_{SLURM_job_id}_{phenotype_number}.o

Prerequistes for a Manhattan/peptide association plot are

  • a call to gz() (in 0_utils.sh for protein) for a compressed DR-filtered data.
  • ensembl-vep (step 3.2 above)3, for which ceuadmin/ensembl-vep/111-icelake now is the default since partition icelake-himem is called.

The CSD3 icelake module ceuadmin/R/4.3.3-icelake now works as smoothly as ceuadmin/R for cclake.

Footnotes

  1. Association

    Accidentally, they were removed for the benchmarks: A1BG, APOB EPCR, ERAP2, PROC. ↩

  2. Location

    {protein}/sentinels/slurm ↩

  3. ensembl-vep

    This is possible since plugin Set::IntervalTree has been made available. For cclake, one uses ceuadmin/ensembl-vep/104. ↩