DNA Internal Control Complex (P6)

[lennythomas]

Does anyone know if the sequence for the DNA Internal Control Complex is available? This is for P6, part number P/N 100-356-500

[rhall]

All PacBio controls are included in SMRT Analysis, both current and historic.
Look in <SMRT Analysis>/common/userdata/references/*control*

If you don't have access to SMRT Analysis let me know and I can post the sequence.

[lennythomas]

I did find the 2kb_control.fasta file there, but was confused because it is actually not 2kb, if you do a `wc 2kb_control.fasta` you see it is actually 53kb+. I attached the file here. If you happen to have the actual 2kb control sequence that would be great if you could share it.

Best,
Lenny

[rhall]

The file is in an unrolled SMRT Bell format (multiple alternating forward and reverse sequences joined by the sequencing adapter). I'm attaching the edited file i.e. repeat, and adapter sequence removed.

[lennythomas]

Perfect. Thank you!

[SillyPoint]

rhall, while we're on the subject of controls...

At what point are the control reads identified and removed from the data stream? Is that done during the processing on the instrument? Are the control reads made available for later processing, if I want to do some sort of error analysis?

Thanks,

--SP

[rhall]

Control reads are only removed in secondary analysis, and even then it depends on the protocol. HGAP Assembly by default does not remove the the control, so it can be used as a control for the assembly procedure. Resequencing and filtering protocols remove the control by default, but this behavior can be changed.

[davisc]

Where can I get information about how this was constructed... I take it, it is a single defined sequence (form the fast file), but was it derived from a plasmid or SMARTBell adapter and ligation...?

In other words, is there a wet-lab description of how this was made somewhere? Could this be done with a range of insert sizes easily? Does it contain a single priming site? Is this insert barcoded? What organism is the sequence (human, alien, tree, etc...)?

Any info would be helpful?

Thanks.