I have a problem using GeneTrack on the public Galaxy server at PSU. There is a server connection error. Is there anybody experiencing the same problem?
Sorry about that - I am supposed to be running that server but it turned out to be way too much additional work. They should actually turn off that tool altogether as it is not supported anymore.
A freshman student (for full disclosure he also happened to be my son interning with another lab ;-) ) has implemented the GeneTrack peak caller as a command line tool, and I would recommend that:
Thanks for your reply. Command line is fine to me. I'm just wondering it has the same algorithm as before. It looks that it only accepts GFF format as input for now according to the README. The comment in the source mentioned bed format as an input, though.
Anther question is about exclusion parameter. Please correct me if I'm wrong. The default is 20. I think the Galaxy version didn't have that parameter. The output nucleosome positions were not overlapped with 147 bp length. I might be wrong. What number do you recommend for nucleosome peak calling?
For the Galaxy version, the output had the same start and end coordinate for bed format. I believe the start should be 1-less because bed format has 0-based coordinate.
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version 2.3.6
(please add your followups as comments not as new answers)
the 20 is the smoothing factor (gaussian kernel width), think of it as the window over which the averaging takes place. The smaller the window the more sensitive the method but it also uses less data to average. A window of 20 for a feature that spans over 140bp is fine in general The Galaxy version as I said is not supported in any way so I can't comment what it produces or even why. I can't access the code that runs it.