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CHU-ULg-Genetic: Exomes vs. Panels.

Final Evaluation using the first validated genes list (CHU Liège; Neuro-Clinicians)

Version: CUGD_V1i1 (2016SEP)

Here below are some files used/generated along this analysis.

Part I. (preparation of input files, run of Perl Code n°1 + LiftOver)

CUGD_v1i1 MS-Excel file: Click Here. (provided by J-H. Caberg)

CUGD_v1i1 used tab delimited genes list: Click Here (remark: removal of ncRNA genes: RMPR & RNUATAC as not covered by Agilent Kits/Probes).

NCBI Txt files (3 per Gene): FASTA, Genbank & NCBI Summary Report ( Click Here for a ZIP file)

Perl Code generating output files: Click Here.

Powerpoint Presentation Documenting Run and LiftOver conversions HG38 to HG19. Click Here.

HG38 BED files (Compatible  UCSC Liftover  software)

HG38 Genes BED file: Click Here.

HG38 Codex BED file: Click Here.

HG38 Tables

HG38 Genes Table: Click Here.

HG38 Codex Table: Click Here.

HG19 BED files (conversion using UCSC Liftover )

HG19 Genes BED file: Click Here.

HG19 Codex BED file: Click Here.

Agilent SureDesign CUGDv1i1 (798 genes submitted, 7 missing)

Report: Click Here.

Targets: Click Here.

BED Files:

AllTracks Click Here.

Covered Click Here.

Regions Click Here.

BED Files (HG19) for Agilent Exome V5 et Exome V6r2.

V5 AllTracks Click Here.

V5 Covered Click Here.

V5 Pagged Click Here.

V5 Regions Click Here.

V6r2 AllTracks Click Here.

V6r2 Covered Click Here.

V6r2 Pagged Click Here.

V6r2 Regions Click Here.

Agilent ClearSeq Inherited Diseases BED Files (+ improved version LeonorPalmeira)

CSID AllTracks Click Here.

CSID Covered Click Here.

CSID Pagged Click Here.

CSID Regions Click Here.

ImprovedCSID Targets Click Here.

More to come...

Part II. Comparisons BEDtoBED.

Compressed Zip containing all input/output files + Perl Codes. Click Here.

Results: Summary (pptx) Click Here.

Results: MS-Excel Workbook Click Here.

Part III.

Compiling Genes Info. from FASTA and Genebank input files (plus Blast Homology Research).

Exons Table. MS-EXCEL (French version). Click Here.