polyprojectNGS

All
Exome
Genome
Target
RNAseq
SingleCell
Amplicon
Other

New Run

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All
Exome
Genome
Target
RNAseq
SingleCell
Amplicon
Other

Group

User

Unassigned

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Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Double click on grid row to Edit

Double click on grid row to Edit

All

Exome

Genome

Target

RNAseq

SingleCell

Amplicon

Other

Refresh

Plateform

Add/Edit Plateform, Update Default

Machine

Add/Edit Machine, Update Default

Sequencing
Method

Add/Edit Sequencing Method, Update Default

Alignment
Method

Add/Edit Alignment Method, Update Default

Calling
Method

Add/Edit Calling Method, Update Default

UMI

Add/Edit UMI

Pipeline
Profile

Add/Update Pipeline Profile

Genome
Release

Edit/Update Genome Release Default

Exon
Capture

Edit/Update Exon Capture Default

User

NEW RUN Species NEW PATIENT

Short Cut for Methods
Use Pipeline Methods to get methods in Alignment,Calling and Other (SV,SPLICES,...) needed in Pipeline
New Pipeline Methods in New Data

Run Name: bcl directory (date_machine_n°run_n°FC+Idflowcell)
Plateform Run Name: fastq directory

Name (bcl)

Plateform Run Name (fastq)

Number of patient

Flowcell A B None

Type

Description no accent, no apostrophe

Profile

Sequencing Plateform Def

Plateform Name

Pileline Profile

Alignment Method Def

Method Name

Calling Method Def

Method Name

Other Method

Method Name

Sequencing Machine Def

Machine Name

Sequencing Method Def

Sequencing method Name

Genome Release Def

Exon Capture from Genome Release Selection Def

Upload the Sample Sheet File before submitting
Run Name and Plateform Run Name must be filled in at least

Upload Sample Sheet

Upload File    Copy/Paste

Column Tabulated List with Header must contain either:

At least, 1 column with Header: Patient

At max, 11 columns with Header Patient first then no order: Patient Group Family Father Mother Sex Status BC BC2 IV Person

IV: Identity Vigilance

Person: Reffering Person Name

Upload Patient Tab File

The Tabulated Header must contain:

first field : Patient

Max: 11 fields, first field: Patient, then other field: no order

Patient Group Family Father Mother Sex Status BC BC2 IV Person

IV: Identity Vigilance

Person: Reffering Person Name

Example of desired columns Patient Sex IV:
Patient Sex IV
Pat1 1 221331133321133
Pat2 2 132231233331113

Column Tabulated List with Header: (Copy/Paste from your Excel File)
Patient  Group  Family  Father  Mother  Sex  Status  BC  BC2  IV  Person

Clear selection

Reset filter

Refresh

Add User

Remove User

Project's Users

List of Users
For a new User:
Use Button New User, then Refresh the List of Users
Group STAFF is added by default

Remove User

List of Users

Deposit: Create a project pedigree file in the project folder
        Force: make a copy version pedigree file and replace it if this already exist
Retrieve: Get pedigree file from project folder to update patient features

Deposit: Create a project somatic file in the project folder
        Force: make a copy version somatic file and replace it if this already exist

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Selector for Patient Control or Not
Submit Button for selected Patient according to Patient Control Selector

Pedigree Folder
Deposit

Retrieve
Project Somatic Folder
Deposit

Save

Remove Patient

Save Project: Phenotype
Use the dropdown list to add or remove phenotype from project and their patients
Add multiples phenotypes: Save one by one the selected phenotype
Remove all phenotypes: Use selection "No Phenotype"

Del Project

Save

Preview/Save All : right click on the Grid

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Toggle to show Table Person Information

Selector for Patient Control or Not
Submit Button for selected Patient according to Patient Control Selector
Update Patients by Copy/Paste

Current Project

Target Project

Refresh

Save

Del Patient

Add Patient

Up Patient

Add IV

Save

Add Document

Refresh

Double click to get the document

Document

Run :

Submit

New Project

Submit

Close

NEW PROJECT

When Toggled, Project will be seen on PolyDejaVu

When Toggled, Project will concern Somatic Cells in molecular Oncology

Description Project no accent, no apostrophe

Genome Release

Phenotype

Capture Id:

Capture Type:

Genome Release:

Folder_out:

Folderout:

Capture Column Tabulated List
chr[1..22,X,Y] *  Start  End
Primer Column Tabulated List
4 Columns: chr[1..22,X,Y] *  Start  End  Pool   Or
6 Columns: chr[1..22,X,Y] *  Start₁  End₁  Start₂  End₂  Pool
* First column: Chromosome column must be confirm to Genome Fasta index File (.fai) of the release

Upload File    Copy/Paste

Column Tabulated List (Copy/Paste from your Excel File)

Submit

Submit

Plateform Name

Submit

Machine Name

Machine type name

Submit

Umi Name

UMI mask

Submit

Sequencing Method Name

Submit

Alignment Method Name

Submit

Calling Method Name

Submit

Save

Pipeline Name

Content

List of Methods

File to Upload:

File to Upload:

File to Upload:

USERNAME

PASSWORD

Sign in

Submit

Year

Submit

Year

Submit

Year

Submit

Year

Submit

Year

Submit

Year

Show

Year Analyse

Submit

Add Group

Remove Group

Click on User icon to get all users of the group
Group STAFF is added by default, no need to select it

Project's Group

List of Groups

User Group

Capture
Save

Gene Release from Capture, not from Bundle

Name

Description

Type

UMI

Method
Version

Genome Release

SELECT a Release Genome and SAVE

Gene Release

Analyse & Validation

Exome Genome SingleCell Validation

Old

New

RNAseq Amplicon Other

Analyse

Validation

Upload Files

Capture File Name

Primer File Name

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Add to Capture

New Bundle & Transcript

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Double click on grid row to Edit Bundle & New Transcript

Remove

Add Bundle

Exon Transcript Site Matching with Exon Capture Position

Exon Transcript Site NOT Matching with Exon Capture Position

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Toggle Switch Filter Exon
Exon of designed Transcript in Exon Capture (covered)
Exon of designed Transcript out Exon Capture (not covered)

Filter Position
Widened Exon Capture position in Start(-) End(+) position from 10 to 50 nt

Deposit
Generate in background an Covered Exon File according Selectors: Switch Filter Exon, Widened Exon Capture position
Retrieve
When the processing on Covered Exon is over, get view from the pre-filtered Covered Exon File

Reset Search

Widened
Capture Position

0

±10

±20

±30

±40

±50

Deposit

Retrieve

Filter Position
Widened Exon Capture position in Start(-) End(+) position from 10 to 50 nt

Only right table
Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Filter Transcripts
Only encoding transcript

Coverage greater than %Threshold (by default 40%) between probes and exons of transcripts

Expand All

Collapse All

Widened
Capture Position

0

±10

±20

±30

±40

±50

% Threshold

Capture:   Id:   Type:   dirTrs:

Save

Submit

Save

Remove

Refresh

Add

Gene Release from Bundle, not from Capture

Bundle ID

Bundle Name

Version

Description
no accent, no apostrophe

Mesh Id

Gene Release

Preview/Save All : right click on the Grid
Preview/Save Selected :Select rows then right click on one Grid row selected

Bundle with at least One Non-annotated Gene Transcript
Bundle with All annotated Gene Transcript

BUNDLE TRANSCRIPT

NEW TRANSCRIPT

AR Autosomal Recessive
AD Autosomal Dominant
XL X Linked

TRANS Transcript Transmission Mode
BTRANS Specific Bundle Transcript Transmission Mode
AR Autosomal Recessive
AD Autosomal Dominant
XL X Linked

Transmision Mode in Trans B-Trans

Copy/Paste Upload File

Upload Transcript Tab File

The Transcript File must be a Text or CSV File without Header
Transcript Column Tabulated List
ENST transcript name (+ eventually Transmission Mode AR or AD or XL)

Column Tabulated List eventually with TRANSmission Mode (AR,AD,XL)

NEW PATIENT INFORMATION Species

Number of patient

Flowcell A B None

Type

Profile

Pileline Profile

Alignment Method Def

Method Name

Calling Method Def

Method Name

Other Method

Method Name

Genome Release Def

Exon Capture from Genome Release Selection Def

NEW PATIENT

Upload File   Copy/Paste

Upload Patient Tab File

The Tabulated Header must contain:

first field : Patient

Max: 11 fields, first field: Patient, then other field: no order

Patient Group Family Father Mother Sex Status BC BC2 IV Person

IV: Identity Vigilance

Person: Reffering Person Name

Example of desired columns Patient Sex IV:
Patient Sex IV
Pat1 1 221331133321133
Pat2 2 132231233331113

Column Tabulated List with Header: (Copy/Paste from your Excel File)
Patient  Group  Family  Father  Mother  Sex  Status  BC  BC2  IV  Person

Only Update Patients
The Tabulated Header must contain:

first field : Patient

Max: 11 fields, first field: Patient, then other field: no order

Patient Group Family Father Mother Sex Status BC BC2 IV Person

IV: Identity Vigilance

Person: Reffering Person Name

Example of desired columns Patient Sex IV:
Patient Sex IV
Pat1 1 221331133321133
Pat2 2 132231233331113

Species

Column Tabulated List with Header: (Copy/Paste from your Excel File)
Patient  Group  Family  Father  Mother  Sex  Status  BC  BC2  IV  Person

Upload File   Column List

The Tabulated Patient Identity Vigilance File must contain
2 columns with Header in order: Patient IV

Upload Patient Identity Vigilance Tab File

Column Tabulated List with Header must contain:

2 columns: Patient   IV

Patient:   Patient Name

IV:   Identity Vigilance   15-digit from 1 to 4, giving the genotype of the 15 SNPs by numbers

1:   wild allele

2:   homozygous alternative allele

3:   heterozygous alternative allele

4:   uninterpretable

Example
Patient IV
Pat1 312323332312321
Pat2 322222112231232
Column Tabulated List with Header: (Copy/Paste from your Excel File)
Patient   IV

Explored Period:
Start Period: One week ago

Preview/Save All : right click on the Grid

For User's Project Manager: Please select Projects befor using Button User

Remove User for All projects
Next

File to Upload:

Select All Person for   Old   New   Clear