Run RawTools for quality control for Linux
To run the quality control analysis with RawTools, we will use the same raw data file that we used previously for the parsing and quantification analysis. For this walkthrough we are using Terminal on your Linux machine.
First navigate to the RawTools directory. We are still using the home folder location on our system.
$cd /home/[username]/RawTools/[RawTools folder]
There are many parameters for the QC analysis with RawTools. Let's first do a basic QC analysis with no database search.
$mono RawTools.exe -d /home/[username]/RawTools/RawTools-master -qc /home/[username]/RawTools/RawTools-master/qc_output/
In the command above, the -d flag is telling RawTools the directory to look for raw files. Every file in the specified directory will be processed to a single output. The -qc flag is telling RawTools where to write the output data. This folder does not need to exist prior to the analysis. The Terminal output should appear similar to below:
Within the qc_output folder, a QC.xml tracking folder and a QcDataTable.csv that contains the summarized outputs will both be made. For further details on how to interpret the QC output, please visit the descriptive page.
To perform a QC analysis with a database search, we will need to use a few more parameters. You will also need a fasta sequence database. We will be using a human database from UniProt. Input the command below:
$mono RawTools.exe -d /home/[username]/RawTools/RawTools-master -qc /home/[username]/RawTools/RawTools-master/qc_output_wSearch/ -db /home/chughes/RawTools/RawTools-master/uniprot_human-crap_sep2018_FWD.fasta -fmods 57.0214@C -vmods 15.9949@M -N 1000 -X /home/chughes/software/xtandem/bin
In this command, -X gives the directory containing the X! Tandem binary and -db input is giving the path to the fasta database to use in the IdentiPy search. This should just be a normal forward database, with no decoy sequences. The -fmods is giving the fixed modification to the X! Tandem search. The -vmods are variable modification inputs. The Terminal output should appear similar to below:
As above, for further details on how to interpret the QC output, please visit the descriptive page.