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CHU-ULg-Genetic: Exomes vs. Panels.

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

DG25 Selected Genes (749 genes) related files.

Input files:

DG25 version 20160628 provided by J-H. Caberg (Tab delimited Txt file recovered from PDF; 2 fields = Gene Expected HGNC name & User Annotation). Click Here.

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

More to come...

For more info. about these files please contact: Pierre.Lecocq@chu.ulg.ac.be

Output files (all except HG19 BED files) have been generated by the main Perl code.

HG38 BED files (compatible UCSC Liftover software).

HG38 Genes BED file: Click Here.

HG38 Codex BED file: Click Here.

Remark: Codex stands for: CODing regions of EXons (taken individually). For Genes encoding protein(s) Codex Sequence(s) encompass the coding region(s) from Methionine up to and inclusive the first Stop codon. For genes encoding ncRNA, Codex sequences encompass fully this ncRNA.

HG38 FASTA files (classic FASTA format for multiple sequences).

HG38 Genes FASTA file: Click Here.

HG38 Codex FASTA file: Click Here.

HG38 CDS FASTA file: Click Here.

Remark: CDS Sequences are ordered concatenations of Codex Sequences corresponding to existing transcripts (mRNA).

HG38 Tables (Tab Delimited Txt files for e.g. Oracle DB)

HG38 Genes Table: Click Here.

HG38 Codex Table: Click Here.

HG38 CDS Table: Click Here.

Alternate Used Name(s) for HGNC Name (Table): Click Here (cancelled).

HG19 BED files (generated via UCSC Liftover)

HG19 Genes BED file: Click Here (1 missing Gene over 749: Click Here)

HG19 Codex BED file: Click Here (15 missing Codex over 14158: Click Here)

Main Perl Code: Click Here.

Next Step: HG19 BED comparison Agilent SureSelect Inherited Diseases(ASID) vs. Ulg-CHU Genetic Diseases (UCGD) genes list.

Summary (powerpoint pptx presentation): Click Here.

MS-Excel evaluation workbook: Click Here.

Remark: Password protected but if required just type nothing ;-)

UCGD Codex Specificity (Blastn vs. HG38; Codex length > 20 nucleotides)

Codex Specificity (MS-Excel workbook): Click Here.

Snapshot (pptx) Exomes vs. Panels (Thresholds on Coverage): Click Here.

Targeting Selected Genes (Coding Exons).

Exomes vs. Panels: Presentation 20160914. Click Here.

More to come...