RDES-TableShaper

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Modify
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Load table file

Table file (.tsv, .csv or .txt)

Or copy & paste here and click somewhere else

Select column separator for import

Tab (\t - Found: -)

Comma (, - Found: -)

Semicolon (; - Found: -)

Colon (: - Found: -)

Table after import

Load settings JSON file (.json)

Load predefined settings

Settings to reshape the table

Select PCR type:

Settings identifier:

Replace all commas by dots

Settings to extract the fluorescence data block

Number of heading rows to ignore:

Number of rows to ignore between values:

Number of rows to keep (maximal):

Extract fluorescence information from column:

Extract melting data by position

Number of heading columns to delete:

Number of colums to keep (maximal):

Settings to extract data

Extract cycle (Amp) or temp. (Melt) data from row:

Apply regex (use "([0-9\.]+)" for Meltcurve):

Extract cycle (Amplification) or temperature (Meltcurve) information from column:

Apply regex (use "([0-9\.]+)" for Meltcurve):

Extract well information from column:

Apply regex:

Extract sample information from column:

Apply regex:

Extract sample type information from column:

Apply regex:

Extract target information from column:

Apply regex:

Extract target type information from column:

Apply regex:

Extract dye information from column:

Apply regex:

Extract Cq or Tm information from column:

Apply regex:

Select columns on col values (-1 selects all):

Apply regex (must be true to be removed):

Table after reshaping

Create RDML file

Experiment ID:
Run ID:
PCR Format - Columns:
PCR Format - Column Label:
PCR Format - Rows:
PCR Format - Row Label:
PCR Format - Predefined:

Complement columns 1 to 5 (required)

Start at well (leave empty for all):

Stop at well (leave empty for only start well):

Text to enter (leave empty for unique id):

Table for export

The columns 1-6 must be filled for successfull import into RDML. Leave them free for empty wells.
White rows indicate missing information, only green rows are complete for import.

Application Description

RDML-TableShaper is a tool to shape tables with amplification data for the import with RDML-tools. This is error-prone and second best to original RDML export by the machine. As some machines do not offer RDML export, TableShaper might help. Most qPCR machines export Excel files. Please convert them by opening in Excel (Microsoft) or Calc (Libre Office), selecting the table with the amplification data and save as tab separated text file. The tab separated text file can be modified using TableShaper.

The use of TableShaper

TableShaper follows three consecutive steps:

1. The table separators have to be identified on the first tab. If it does not work out automatically, the separator has to be selected manually. The table columns need to be recognized in the table below.

2. The content need to be recognized in the second tab. If your table format is not found in the predefined settings, you may iteratively select the parameters and load / save them for later use. Adapt the "Number of columns to keep" and "Number of rows to keep" to match the experiments cycle and well numbers and avoid cutoff. "Settings to reshape the table" is the most dramatic shaping option. You can opt to flip the table or to build a table from value list. The result is drawn below and can be used to select the columns for data extraction.

3. Fill the missing content in the third tab. To be able to import the table into RDML, the first six columns have to be filled. Using the fields on the third tab eases this step as squares B2-D7 can be used. Take care in this step as errors in the target id and sample id can not be fixed in RDML later. Save the result as .tsv file.

4. To create an RDML file fill the information on the "Create RDML file" card and hit the button. RDML-Edit will open with the created RDML file and allow to save or view the RDML file.
Alternatively the data can be imported int existing RDML files. Open the RDML file in RDML-Edit (or create new) and enable editing with the "enable edit mode" button. Now change to the experiments tab and open an experiment or create a new experiment. In the experiment, create a new run. Take care to set the ID and PCR-Format fields correctly. Now select the exported .tsv file in "Import Amplification Data". Once saved you can inspect the result using RunView or save it as RDML file on the first tab.

Accepted Input

The table files can be provided in text format with tab, comma or semicolon as separator(*.txt, *.tsv, and *.csv).

Sample Data

The "Show Example" button loads an example table file (click to download file) from a BioRad iCycler v9.35.

More Help

A general help file is available as RDML-Tools Help.