Hello,
If I can resurrect this thread briefly, I've been having a little trouble with ERANGE 3.1. When I try to either annotate the genes or use the getfasta.py script to get the fasta sequence for meme, I always and up with a blank file. The annotation script gives no errors, and the getfasta.py script only says there is a problem for each peak. Everything is "installed" properly, and my $PATH variable is set, so that isn't the issue. In looking through the code, I see a call to "Genome', but I haven't been able to locate that anywhere in the code. This might be an issue more with cistematic than with ERANGE, or it's just me missing the obvious fix. Either way, any suggestions would be wonderful. I've already written Perl scripts for some of this, but I'd like to save time and use the built-in scripts if possible. Thanks so much!
Daniel
EDIT: It was a result of a difference in the input file. The eland files I was using were slightly different than normal; everything works as it should now!
If I can resurrect this thread briefly, I've been having a little trouble with ERANGE 3.1. When I try to either annotate the genes or use the getfasta.py script to get the fasta sequence for meme, I always and up with a blank file. The annotation script gives no errors, and the getfasta.py script only says there is a problem for each peak. Everything is "installed" properly, and my $PATH variable is set, so that isn't the issue. In looking through the code, I see a call to "Genome', but I haven't been able to locate that anywhere in the code. This might be an issue more with cistematic than with ERANGE, or it's just me missing the obvious fix. Either way, any suggestions would be wonderful. I've already written Perl scripts for some of this, but I'd like to save time and use the built-in scripts if possible. Thanks so much!
Daniel
EDIT: It was a result of a difference in the input file. The eland files I was using were slightly different than normal; everything works as it should now!
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