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Hi guys,
I have been provided with two 454 sequencing de novo assemblies, which were created with Newbler 2.3. We do plan to reassemble the reads on our own as soon as we get access to a PC powerful enough, but in the mean time I was hoping to have a look at the flowgrams for our reads.
It is my understanding that I'll be able to see the flowgrams for each read if I open up the assembly project in gsAssembler. I don't know of any other way to view the flowgrams (although I have extracted the .flow file with sffinfo, I just don't know of any programs that will show it me in graph form). If there are other programs out there that can show me that data, please let me know.
However, I have installed the Roche 2.8 data analysis programs on my laptop (Ubuntu 12.10) and receive the following error when I open the projects:
At this point, the alignment files and flowgram tabs are greyed out, although the other tabs display as expected.
The read files have been moved in the sense that the entire working directory assembly has been moved to this computer, although as far as I'm aware the structure within that directory is the same. (I have no way of knowing, however).
I did search google already, and it was suggested that not having read/write permissions for the assembly directory might be the problem. However, I ensured that I did have that permission for the assembly directory and it did not solve the problem.
So, is there any way for me to fix this problem without reassembling the data? I'm doing this on my own personal laptop, so reassembling is out of the question.
I have been provided with two 454 sequencing de novo assemblies, which were created with Newbler 2.3. We do plan to reassemble the reads on our own as soon as we get access to a PC powerful enough, but in the mean time I was hoping to have a look at the flowgrams for our reads.
It is my understanding that I'll be able to see the flowgrams for each read if I open up the assembly project in gsAssembler. I don't know of any other way to view the flowgrams (although I have extracted the .flow file with sffinfo, I just don't know of any programs that will show it me in graph form). If there are other programs out there that can show me that data, please let me know.
However, I have installed the Roche 2.8 data analysis programs on my laptop (Ubuntu 12.10) and receive the following error when I open the projects:
Unable to launch back-end programs to read alignment results.
This usually occurs if the project is in use by another instance of the program, if a computation of the project is being run from the command line, or if one or more of the project's read files have been moved from their original locations.
If that is not the case, then some data indices may be in an inconsistent state.
Performing a full (non-incremental) analysis may remedy the situation.
If not, please report this error to your customer support representative.
This usually occurs if the project is in use by another instance of the program, if a computation of the project is being run from the command line, or if one or more of the project's read files have been moved from their original locations.
If that is not the case, then some data indices may be in an inconsistent state.
Performing a full (non-incremental) analysis may remedy the situation.
If not, please report this error to your customer support representative.
The read files have been moved in the sense that the entire working directory assembly has been moved to this computer, although as far as I'm aware the structure within that directory is the same. (I have no way of knowing, however).
I did search google already, and it was suggested that not having read/write permissions for the assembly directory might be the problem. However, I ensured that I did have that permission for the assembly directory and it did not solve the problem.
So, is there any way for me to fix this problem without reassembling the data? I'm doing this on my own personal laptop, so reassembling is out of the question.
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