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Forum: Pacific Biosciences 06-21-2013, 09:05 AM
Replies: 17
Views: 11,735
Posted By sagarutturkar
What type of pacbio reads are recommended for...

What type of pacbio reads are recommended for PBJelly? So far, I was using native Pacbio files - i.e. f(iltered.subreads.fasta). However, If I use corrected PacBio reads, would that be beneficial or...
Forum: Pacific Biosciences 02-27-2013, 05:28 AM
Replies: 17
Views: 11,735
Posted By sagarutturkar
Oh yes! That's true. I just made a generic shell...

Oh yes! That's true. I just made a generic shell script to run PBJelly and forgot about different steps. You are right! :)
Forum: Pacific Biosciences 02-27-2013, 05:17 AM
Replies: 17
Views: 11,735
Posted By sagarutturkar
Thanks for this suggestion. But I guess PBJelly...

Thanks for this suggestion. But I guess PBJelly always run blasr/mapping step in order to fill the gap. So, may not be feasible to change the time.
Forum: Pacific Biosciences 02-26-2013, 06:56 AM
Replies: 17
Views: 11,735
Posted By sagarutturkar
Well, Replying to my own thread. It might be...

Well,

Replying to my own thread. It might be useful for others to know. Seems like the PBjelly is not yet optimized to make full use of available memory. There might be some memory leaks in python...
Forum: Pacific Biosciences 02-19-2013, 05:29 AM
Replies: 17
Views: 11,735
Posted By sagarutturkar
PBJelly

Hi,

I have SMRTanalysis and PBJelly package installed. I was able to run the PBJelly with test data provided with software. However, when I was running it for a bacterial genome which is (~10 MB...
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