If you run the Sequest search through the TPP GUI interface or via the runsearch.exe wrapper on the command line, it would pack up and compress the search results folder and delete the corresponding directory (of dta/outs). You obviously don't need to keep the folders around if you have no use for those files. My suggestion would be to compress the .out files into a zip or tgz archive and then delete each directory only because the searches are expensive and there is esoteric bits of info in those files that aren't replicated in a pep.xml. If you do archive those files in a .tgz in a specific way, the link to the out files in the PepXML Viewer can still display the search results pulling the info directly from the compressed archive. You don't need to include the .dta files in the compressed archive because those spectra are easily recreated from the mzXML and the spectral display tool will grab corresponding spectrum from the mzXML file if present.
On Wed, Sep 16, 2009 at 1:32 PM, Kris <ktrunc...@gmail.com> wrote: > > Anyone know what I need the intermediate folders for? > > -Kris > > On Sep 10, 4:49 pm, Kris <ktrunc...@gmail.com> wrote: >> Hi, >> >> I'm running a lot of database searches on a large number of mzXML >> files. Because of this, I need to conserve space on my computer. My >> understanding of the software is that "Database Search" generates afolderof >> out/dta files, which is converted to a PepXML file. The >> PepXML file is then used in "Analyze Peptides" to generate probability >> scores for matches. >> >> My question is: Is there any reason why I would want to save the >> folders of out/dta files? It seems like the only thing these folders >> are used for is generating PepXML files, and having the PepXML files >> is all I need. >> >> I would like to delete the folders of out/dtas to save space on my >> computer. But if there is some reason I should save them (something >> they could be used for later on), please let me know. >> >> Also, I noticed that if you run a large number of mzXML files in >> "Database search", the search usually freezes after it gets to about >> 2.5 million lines of output (I believe). So, I've been running the >> commands in command line. Please let me know, if you see any problem >> with this. >> >> Thanks, >> Kris > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
