Hi Marc
I am testing your program and noted minor things, but in general exerything
works and is superfast (on Arch Linux runnin on an Intel i7 with 32 Gigs of
RAM)
README
tar -xzf unpacks .tar.gz files in a oneliner
DOCUMENTATION
It would be instructive to document the file structure that the genbank
files should be provided in.
In the editor for the bins the choice how the taxa on the right side are
sorted - either alphabetically as they are initially, or by relevance, is
not documented.
There is no save edits button in the Editor window. You have to press the
Commit button
SIDENOTES
on Glimmer dependency
With the 2 files you provide from the Glimmer package the dependency check
is now OK. Just for curiosity I checked and simple-score is not included in
the Glimmer3.02 I downloaded and compiled... there is a file that is called
score-fixed which basically does the same. Which Glimmer did you compile v2
or v3 and should therefore be available?
TYPOS
There is a typo in the Dependency check failed window that opens up - there
Glimmer is mispelled "Glimer".
BUGS
in the Bin Editor the contigs are plotted GC vs. coverage i think that GC
content is underestimated compared to my own calculations - could it be
that you are not correcting for Ns that can be quite numerous in the velvet
scaffolds
FEATURE REQUESTS
1) In the GC vs. Coverage plots a selection of the plotted contigs by
length
could create much cleaner contig clusters for the well-assembled contigs -
E.g. by having a slider that allows the user to set the minimal contig
length af the contigs to be displayed up to 1000 or 5000 nt
2) Once you select a range of contigs with control+clicking and dragging
there is no simple way back to all contigs, except zoomin all out and
marking the whole plot. A button e.g. "all contigs" would be convenient
3) If I scale the editor window the subwindows are stuck at certain sizes,
not using the space provided
thats it for now, more to come...
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Harald,
thank you once more for your valuable input and testing.
Requests for changes to/additional documentation have been added to the wiki
The "Commit" button will be relabeled as "Save Edits" in the next version.
Type has been corrected
For the calculation of the GC content, check out the code here. This algorithm not be affected by N's. I compared the results with an online GC calculator and it gave the same results...
About the absence of simple-score in the glimmer package, that is a very interesting one. I used the glimmer version 3.02 that was provided with the SCIMM binner. It is available from here. Apparently, the authors have added the program "simple-score" specifically for the purpose of binning and it is not included in the standard distribution... I was not aware of this and will find a solution...
Feature requests: 1) will be added to next version; 2) Already there, documentation updated. 3) May be added to the next version, I still find the correct and dynamic sizing of custom swing widgets a challenge...
Last edit: Marc Strous 2012-11-16
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Marc
I am testing your program and noted minor things, but in general exerything
works and is superfast (on Arch Linux runnin on an Intel i7 with 32 Gigs of
RAM)
README
tar -xzf unpacks .tar.gz files in a oneliner
DOCUMENTATION
It would be instructive to document the file structure that the genbank
files should be provided in.
In the editor for the bins the choice how the taxa on the right side are
sorted - either alphabetically as they are initially, or by relevance, is
not documented.
There is no save edits button in the Editor window. You have to press the
Commit button
SIDENOTES
on Glimmer dependency
With the 2 files you provide from the Glimmer package the dependency check
is now OK. Just for curiosity I checked and simple-score is not included in
the Glimmer3.02 I downloaded and compiled... there is a file that is called
score-fixed which basically does the same. Which Glimmer did you compile v2
or v3 and should therefore be available?
TYPOS
There is a typo in the Dependency check failed window that opens up - there
Glimmer is mispelled "Glimer".
BUGS
in the Bin Editor the contigs are plotted GC vs. coverage i think that GC
content is underestimated compared to my own calculations - could it be
that you are not correcting for Ns that can be quite numerous in the velvet
scaffolds
FEATURE REQUESTS
1) In the GC vs. Coverage plots a selection of the plotted contigs by
length
could create much cleaner contig clusters for the well-assembled contigs -
E.g. by having a slider that allows the user to set the minimal contig
length af the contigs to be displayed up to 1000 or 5000 nt
2) Once you select a range of contigs with control+clicking and dragging
there is no simple way back to all contigs, except zoomin all out and
marking the whole plot. A button e.g. "all contigs" would be convenient
3) If I scale the editor window the subwindows are stuck at certain sizes,
not using the space provided
thats it for now, more to come...
Dear Harald,
thank you once more for your valuable input and testing.
Requests for changes to/additional documentation have been added to the wiki
The "Commit" button will be relabeled as "Save Edits" in the next version.
Type has been corrected
For the calculation of the GC content, check out the code here. This algorithm not be affected by N's. I compared the results with an online GC calculator and it gave the same results...
About the absence of simple-score in the glimmer package, that is a very interesting one. I used the glimmer version 3.02 that was provided with the SCIMM binner. It is available from here. Apparently, the authors have added the program "simple-score" specifically for the purpose of binning and it is not included in the standard distribution... I was not aware of this and will find a solution...
Feature requests: 1) will be added to next version; 2) Already there, documentation updated. 3) May be added to the next version, I still find the correct and dynamic sizing of custom swing widgets a challenge...
Last edit: Marc Strous 2012-11-16