rgiessmann / peaks

Python toolbox to evaluate capillary electrophoresis chromatograms, intended to detect binding of small molecules to DNA, i.e. to perform footprinting.

peaks

To install:

• Open "anaconda prompt"
• type: pip install git+https://github.com/rgiessmann/peaks

To execute run_* files:

• Download this repository and unzip it to C:\peaks
• Open "anaconda prompt"
• navigate to the folder containing the file called "input_traces.csv" (you can do this by typing: cd ... where ... can be the absolute path, e.g. C:\Users\Robert\Desktop\)
• type: ipython C:\peaks\scripts\run_*.ipy , where you replace * with the filename you want to run

To generate annotation-able csv files

• Check https://gitlab.tu-berlin.de/r.giessmann/fsa_to_csv_converter

To annotate .csv files of analyzed peaks with raw peak heights

• Open "anaconda prompt"
• navigate to the folder containing the .csv files generated by PeakScanner (you can do this by typing: cd ... where ... can be the absolute path, e.g. C:\Users\Robert\Desktop\)
• type: annotate -i <analyzed_peak_file.csv> <raw_peak_file.csv> <raw_peak_file2.csv> ... , where you replace the <...> with the real filenames

Data specifications

Input files

input_traces.csv

tab separated values

File name	Dye color	Ltot concentration (µM)
01-18-16-11-27 AM.fsa	B	0
01-18-16-35-11 AM.fsa	B	5

--> auto-picking of reference trace from all 0M traces?

referenced .csv files of analyzed peaks

comma separated values

| Status|Sample Name|Sample Type|Size Standard|Analysis Method|SQI|Offscale|Quality|UD1|UD2|UD3|Dye|Sample Peak|Sample File Name|Size|Height|Area in Point|Area in BP|Data Point|Begin Point|Begin BP|End Point|End BP|Width in Point|Width in BP|User Comments|User Edit | --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | ---| --- | --- | --- Analyzed|0|Sample|bto 550|Sizing Default - NPP|false|Pass|Pass||||B|1|01-18-16-11-27 AM.fsa||123|1117|0|2065|2052|-1|2072|-1|10|0|| Analyzed|0|Sample|bto 550|Sizing Default - NPP|false|Pass|Pass||||B|2|01-18-16-11-27 AM.fsa||83|911|0|2079|2072|-1|2091|-1|10|0||