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Forum: Pacific Biosciences 11-14-2013, 12:53 AM
Replies: 17
Views: 11,726
Posted By HenrivdGeest
Yes,I also encounter this. I think there is a...

Yes,I also encounter this.
I think there is a small bug in the sample scripts in the latest release of pbjelly(13.10.22). The mapping quality of the reads is lower than the default filtering...
Forum: Pacific Biosciences 06-27-2013, 10:29 PM
Replies: 17
Views: 11,726
Posted By HenrivdGeest
I've never tried pbjelly with clean reads. Since...

I've never tried pbjelly with clean reads. Since most of the time those reads will be shorter, the chance of finding an overlap is also smaller. If there aren't shorter, I would not see any drawback...
Forum: Pacific Biosciences 03-19-2013, 12:27 AM
Replies: 17
Views: 11,726
Posted By HenrivdGeest
I think you should look in the that output log...

I think you should look in the that output log file for "Didn't pass assembly". Those are the assemblies that failed. Could be due to the crash or due to another issue of which I am not aware of :)...
Forum: Pacific Biosciences 02-27-2013, 05:23 AM
Replies: 17
Views: 11,726
Posted By HenrivdGeest
If you run PBJelly, you run the mapping and the...

If you run PBJelly, you run the mapping and the assembly step separately, so you can change the code in between. Or make some if statement in the code itself:)
Forum: Pacific Biosciences 02-26-2013, 11:00 PM
Replies: 17
Views: 11,726
Posted By HenrivdGeest
Hi, I also got this error a few times. But,...

Hi,
I also got this error a few times.
But, its not that its not a problem. The errors you see come from an individual gap closure assembly operation. That one just failed. You can see these failed...
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