search

compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
30 stars 17 forks source link

issue with DeNovoGUI-1.14.5 #15

Closed CarlaCristinaUranga closed 7 years ago

CarlaCristinaUranga commented 7 years ago

Hi, I am not having any luck with DeNovoGUI command line interface. I get the following errors for the identification parameter CLI: denovopar.txt

I get the following error message with the DeNovoGUI CLI: ucd256ma_denovo.txt

I tried un-installing and then re-installing DeNovoGUI-1.14.5 to no avail. Thank you in advance for your help!

Best wishes,

Carla Uranga

hbarsnes commented 7 years ago

Hi Carla,

Thanks for telling us about this. Can you try this beta version of DeNovoGUI to see if it solves the issues: http://vedlegg.uib.no/?id=7080f7010df83e57123adf4612bbd01b?

Best regards, Harald

CarlaCristinaUranga commented 7 years ago

Sure, I love these proteomics tools quite a bit, there are so many shortcuts I wish they had for post-sequencing analysis. I wish I knew how to program! The Beta version did work, except that pNovo is still not activating or working, so I am going with Novor and PepNovo for now. Thanks again.

Best wishes,

Carla Uranga

hbarsnes commented 7 years ago

Hi Carla,

DeNovoGUI v1.15.0 has just been released fixing the issues with the command line.

Best regards, Harald

CarlaCristinaUranga commented 7 years ago

Super sweet, you guys are fast, looking forward to trying it out! Do you guys have any proteomics tools for differential expression? Best wishes and greetings from a member of the science rebellion in Mexico!

On Jan 31, 2017 6:26 AM, "Harald Barsnes" notifications@github.com wrote:

Hi Carla,

DeNovoGUI v1.15.0 has just been released fixing the issues with the command line.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/15#issuecomment-276376700, or mute the thread https://github.com/notifications/unsubscribe-auth/AVXji1UXLQw_ocujw8wJVyjRTLUYl4Zqks5rX0SOgaJpZM4Lo43O .

hbarsnes commented 7 years ago

Hi Carla,

The only thing we have at the moment is Reporter (http://compomics.github.io/projects/reporter.html) for iTRAQ and TMT quantification.

Best regards, Harald

CarlaCristinaUranga commented 7 years ago

So there is nothing for empai yet? Or based on spectral counts?

Best wishes,

Carla

On Jan 31, 2017 6:42 AM, "Harald Barsnes" notifications@github.com wrote:

Hi Carla,

The only thing we have at the moment is Reporter ( http://compomics.github.io/projects/reporter.html) for iTRAQ and TMT quantification.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/15#issuecomment-276381209, or mute the thread https://github.com/notifications/unsubscribe-auth/AVXji_6ov-Hw614zTSDbEtNHkCOJrMbaks5rX0hfgaJpZM4Lo43O .

hbarsnes commented 7 years ago

Hi Carla,

Spectral counting is included in PeptideShaker. You can choose between emPAI or NSAF. See the column called "MS2 Quant".

Best regards, Harald