CLI results

[Catherine Heylings]

Hi, 

I was wondering from the output files created on the DeNovoCLI, how do we process to get a list of predicted peptides? Is there another wiki on this?

Regards, 

Catherine

[Harald Barsnes]

Hi Catherine,

If you run DeNovoGUI in command line mode you will only get the direct output from the individual algorithms. In the graphical user interface there is an option to map the de novo results to the sequences in a FASTA file, but this is not available from the command line.

You may however consider running Novor and DirecTag via SearchGUI, as then you can process the output via PeptideShaker, either via the graphical user interface or the command line.

Best regards,

Harald

[Catherine Heylings]

Thank you for your quick response. We ideally want to change the parameters of each algorithm which is why we want to use the CLI. We are having issues with DirecTag producing very short peptides of 3 aa and this means we are getting a lot of false positive hits. So there is no really way of extracting sequences at all from the CLI. Is there away we can change the parameters of the algorithms?

[Harald Barsnes]

Hi Catherine,

You can change the parameters for via https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI. See for example: https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI#directag-advanced-parameters.

To extract the sequences you have to parse the de novo algorithm output. For DirecTag the output is basically a tab separated text file, so should not be too difficult to extra the sequences? Or am I misunderstanding your question?

Best regards,

Harald

[Catherine Heylings]

Hi Harald, 

I must not be getting the right output, I haven't got a tab text file out. So I'll try and re-run, does the CLI version allow you to run all three at once, I wanted to run the directag, PepNovo and novor. It has only been novor where I have got an output successfully.

Best, 

Catherine

[Harald Barsnes]

Hi Catherine,

> I must not be getting the right output, I haven't got a tab text file out.

For DirecTag you should get a .tags file containing rows with the tags and other related information.

> So I'll try and re-run, does the CLI version allow you to run all three at once, I wanted to run the directag, PepNovo and novor.

You can choose which algorithms to run by using the parameters listed at under optional common parameteres here: https://github.com/compomics/denovogui/wiki/DeNovoCLI.

> It has only been novor where I have got an output successfully.

Keep in mind that Novor always provides complete peptide sequences, while DirecTag only provides tags of the chosen length. Hence you will never get full peptide sequences with DirecTag.