SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
New PacBio system: Sequel SNPsaurus Pacific Biosciences 62 09-28-2017 04:33 AM
Sequel System NA12878 Structural Variant Call Set pacbio Pacific Biosciences 0 12-06-2016 03:38 PM
Sequel System Data Release: Arabidopsis Dataset & Genome Assembly pacbio Pacific Biosciences 3 09-28-2016 01:52 PM
PubMed: Digital gene expression analysis of the zebra finch genome. Newsbot! Literature Watch 0 04-03-2010 02:02 AM

Reply
 
Thread Tools
Old 08-31-2017, 09:12 AM   #1
pacbio
Member
 
Location: Menlo Park, CA

Join Date: Sep 2011
Posts: 53
Smile Sequel System Data Release: Iso-Seq Results for Hummingbird/Zebra Finch Brain Tissue

We’ve just released data from Iso-Seq interrogations of brain tissue from two avian models of vocal learning, Anna’s hummingbird (Calypte anna) and zebra finch (Taeniopygia guttata), sequenced in collaboration with the Erich Jarvis and Olivier Fedrigo labs at the Rockefeller University.

For this data set, we used the Iso-Seq method to characterize the transcriptomes of two birds, with brain total RNA. The two species’ brain samples were barcoded, pooled, and sequenced using 4 SMRT Cells on the Sequel System. An average of ~460,000 reads was generated per SMRT Cell; total sequencing data yields ranged from 6.1 to 7.7 Gb per SMRT Cell. More than 15,000 isoforms were identified in each species, including thousands that had not been previously annotated in each bird and 400 to 500 new genes.

Download the data set & read blog post
pacbio is offline   Reply With Quote
Old 08-31-2017, 04:52 PM   #2
nucacidhunter
Senior Member
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,166
Default

I wonder if you could post screenshot of the Run QC for each SMRT Cell detailing productivity, read length, total bases and movie time from SMRT Link as it can be very useful benchmark for sequencing centers and their clients.
nucacidhunter is offline   Reply With Quote
Old 09-03-2017, 01:52 PM   #3
BioKiwi
Member
 
Location: KiwiTeritory

Join Date: Sep 2014
Posts: 19
Default

Could anyone share their Sequel Run QC of a Iso-seq library. PacBio does not seem keen to share details of what lies behinde their polished data.
BioKiwi is offline   Reply With Quote
Old 09-05-2017, 08:05 AM   #4
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 318
Default

See the attached PDF.
Attached Files
File Type: pdf IsoseqQC.pdf (442.2 KB, 29 views)
rhall is offline   Reply With Quote
Old 09-19-2017, 12:44 AM   #5
weigrc
Member
 
Location: Hong Kong

Join Date: Oct 2011
Posts: 44
Cool

Dear all,

The attached is what we recently done for Iso-Seq application.

We are first time to spike-in Sequel SMRT Cell Control Complex 2.0, anyone knows how to interpret its sequencing data?

Thanks,
Wei
Attached Files
File Type: pdf Iso-Seq_170915.pdf (45.6 KB, 13 views)

Last edited by weigrc; 09-19-2017 at 12:47 AM.
weigrc is offline   Reply With Quote
Old 09-19-2017, 08:02 AM   #6
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 318
Default

The run looks reasonably good. There are 1593 control reads i.e. its only a very small portion of your data (as it should be), and the polymerase read length and concordance for the control look good, 15105 and 0.85 respectively.
The distribution of polymerase read lengths for your sample is a little lower than for the control, which may indicate the sample isn't of extremely high quality, but it isn't a red flag, given you have 6.56 Gb of raw data.
rhall is offline   Reply With Quote
Old 09-19-2017, 01:45 PM   #7
nucacidhunter
Senior Member
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,166
Default

Hi Wei, thanks for posting your run results. I wonder what chemistry and software version you have used. Some versions recommends Magbead loading for Iso-seq libraries.
nucacidhunter is offline   Reply With Quote
Old 09-19-2017, 10:29 PM   #8
weigrc
Member
 
Location: Hong Kong

Join Date: Oct 2011
Posts: 44
Default

Quote:
Originally Posted by nucacidhunter View Post
Hi Wei, thanks for posting your run results. I wonder what chemistry and software version you have used. Some versions recommends Magbead loading for Iso-seq libraries.
We used diffusion loading to keep every size of transcript for sequencing. And refer to below for the versions.

Sequel Sequencing Kit: V2
ICS SW: V5.0.0
SMRT Link: V5.0.1

Thanks,
Wei
weigrc is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:09 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO