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Forum: Pacific Biosciences 06-07-2014, 11:39 AM
Replies: 2
Views: 3,463
Posted By skerker
My mistake -- the wiki docs were confusing. ...

My mistake -- the wiki docs were confusing. HGAP2 already supports genomes up to 130 Mbp. so adding the advanced HGAP protocol isn't necessary in SMRT portal v 2.1 and higher.
...
Forum: Pacific Biosciences 06-07-2014, 11:35 AM
Replies: 2
Views: 3,463
Posted By skerker
Well I figured out the problem -- the .XML file...

Well I figured out the problem -- the .XML file is written for SMRT portal v 2.0 and puts together protocols that no longer exist in the current version of SMRT portal. So it seems that the ability...
Forum: Pacific Biosciences 06-06-2014, 04:03 PM
Replies: 2
Views: 3,463
Posted By skerker
HGAP Advanced Protocol

I'm trying to install the HGAP_Assembly_Advanced.1 protocol - I added the necessary .XML file, but when I run the SMRT portal, I'm unable to make any selections on parameters. Wondering if anyone...
Forum: Pacific Biosciences 06-06-2014, 07:18 AM
Replies: 4
Views: 3,756
Posted By skerker
Thank you - I appreciate the help and advice. ...

Thank you - I appreciate the help and advice.

Jeff
Forum: Sample Prep / Library Generation 06-05-2014, 05:56 PM
Replies: 0
Views: 1,399
Posted By skerker
powerclean Pro

Anybody have experience in comparing powerclean from MoBio with their new powerclean Pro kit? I'm hoping they produce DNA of the same quality, but I was told that only the regular kit has been...
Forum: Pacific Biosciences 06-05-2014, 05:50 PM
Replies: 4
Views: 3,756
Posted By skerker
Thanks for the reply. I haven't found much other...

Thanks for the reply. I haven't found much other information either. I guess I'll just have to play around with ovlThreads=integer (default=2) and ovlConcurrency=integer (default=1) and see what...
Forum: Pacific Biosciences 06-04-2014, 02:25 PM
Replies: 4
Views: 3,756
Posted By skerker
overlapInCore using up all RAM

I have been running RS_HGAP_Assembly.2 in SMRT portal and the job has been failing at the overlapInCore step. I was able to solve the problem by changing the nproc from 64 down to 24 so it would not...
Forum: Pacific Biosciences 06-04-2014, 02:18 PM
Replies: 5
Views: 4,097
Posted By skerker
Thanks for the reply. I'll check with the seq....

Thanks for the reply. I'll check with the seq. center. We are trying again using gDNA that has been purified by a Qiagen Tip 20/G and then with powerclean from MoBio. Hopefully that will do the...
Forum: Pacific Biosciences 05-23-2014, 07:20 AM
Replies: 5
Views: 4,097
Posted By skerker
Thank you for the reply! You did magbead...

Thank you for the reply! You did magbead cleanup of the SMRTbell library? I have been submitting samples to a sequence center, so unfortunately I don't have much control over what gets done, or...
Forum: Pacific Biosciences 05-22-2014, 10:07 AM
Replies: 5
Views: 4,097
Posted By skerker
Problems with gDNA prep for PacBio

Our goal is to prep genomic DNA from S. cerevisiae to make either a 10kbp or 20kbp library. We have been having trouble with sample quality (either contamination or damage?) resulting in short...
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