To do only once: On central-bio, open a unix shell and if not already done, edit the file .profile (in your home directory) and add this line:
module use /pasteur/projets/policy01/Matrix/modules
quit the shell (or source the .profile file).
When you open a new terminal, you should now be able to use the fragment_analyser module. You can load it in your environment as follows:
module load fragment_analyser
Issue with the creation of images:
echo "backend:agg" >> ~/.config/matplotlib/matplotlibrc
Assuming you want to analyse a set of files starting with '2015' with csv extensions, type:
fragment_analyser --pattern 2015*csv
If you do not want to create images, add
--no-images
Results are stored in summary_all.csv and summary_filter.csv files.
There are other options related to the analyse. Please type:
fragment_analyser --help
Input files must be CSV with the 12 wells. The number of files is not important.
The tool fragment_analyser will identify the peak across the 12 samples that are the most relevant. All results will be stored in summary_all.csv. If you expect all peaks to be found at the same location, peaks that are outliers should be discarded. In the file summary_filter.csv the outliers are to NA (empty string). Once a peak is identified, we keep track of its position (Size in base pair), concentration and a quantity refered to as nM.
Usage:
fragment_analyser --pattern files*csv
The file results.csv should contains 4 columns:
Well,Sample ID,Size (bp),% (Conc.),nmole/L,ng/ul,Avg. Size,RFU,TIC (ng/ul),TIM (nmole/L),Total Conc. (ng/ ul),amount (nM) D1,T4,649.0,94.9,11.045,4.3591,716.0,1753.0,4.5912,17.688,4.6007,10.33329382 D2,T7,610.0,91.9,22.672,8.4052,651.0,4773.0,9.1461,44.465,9.1541,21.19848676 D3,P1,667.0,92.7,9.132,3.6994,693.0,1999.0,3.989,20.247,4.0108,8.53281052 D4,Mu,688.0,84.5,3.622,1.5137,678.0,795.0,1.7909,13.168,1.7982,3.384839 D5,rien,,,,,,,,,, D6,rien,,,,,,,,,, D7,rien,,,,,,,,,, D8,rien,,,,,,,,,, D9,rien,990.0,100.0,0.001,0.0006,982.0,20.0,0.0006,0.001,0.0369,0.0009324 D10,rien,,,,,,,,,, D11,rien,,,,,,,,,, D12,Ladder,,,,,,,,,,
The 12th well (Ladder) is always empty.
All columns are copies of input files except for the last column that is the concentration in nM unit. and is computed as:
conc * 1000 / ((Size) * 650 /1000)
where 650 is a hard coded value (mw_dna)
Please see the notebooks directory or the doc directory. The doc directory is a sphinx project and should be compiled for a better rendering. See also the brief but up-to-date documentation using
fragment_analyser --help