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leekgroup / derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data
http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short?rss=1
MIT License
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Where is tophatY-updated? #8

Closed brianhigh closed 9 years ago

brianhigh commented 9 years ago

Hi! I am trying to run your R script analysis_code.R to reproduce your research paper results and when the command...

makeDb(dbfile = dbfile, tablename = tablename, textfile = textfile, cutoff = 5)

...is executed I get this error:

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'tophatY-updated': No such file or directory

I do not see this file tophatY-updated in your repository. Where can I get this file? Can you add it to your repository? Thanks!

alyssafrazee commented 9 years ago

Thanks for the note; apologies for the confusion. I have added a section to the README to make this explicit: the tophatY-updated file is too big to store here (2.2G), so if you want to run my code, you will have to create it yourself based on the data files in data, the countReads.py script, and some R code that I used to merge the results. All of this is now in the README section called "reproducing the manuscript's results". Let me know if there are any problems with this. Thanks!

brianhigh commented 9 years ago

Thanks, I'll try it right now. :)