4/1/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook

Re: SureSelect library structure

Jackson Leong <jleong@gigagen.com>
Tue 3/31/2020 9:16 AM
To: Agilent Informatics Support <informatics_support+id36466@cartagenia.zendesk.com>
Cc: SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com>; NGS.SUPPORT (Shared)
<ngs.support@agilent.com>
Mandar,

We were finally able to analyze the data it just took a while to deciphere. Thanks for your help. 

Jackson

On Tue, Mar 31, 2020, 7:29 AM Mandar Bedse (Agilent Informatics Support)
<informatics_support@cartagenia.zendesk.com> wrote:
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Mandar Bedse, Mar 31, 7:59 PM IST:

Hi Jackson,

Let us know if you need any further help.

Best Regards,
Mandar Bedse
Agilent Informatics Support

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NGS.SUPPORT (A-Santa Clara,exgen1), Mar 27, 2:23 AM IST:

Hi Jackson,

Our data analysis tool can only process Illumina libaries. SureSelect baits only do the enrichment, the libraries
themselves are Nanopore libraries once you add Nanopore adapters. You may have to contact Nanopore support to get
their help on how process them.

Thanks,

Weiwei

Thanks,

https://outlook.office.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAAAAB… 1/6
4/1/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook
Our bioinformatic person tried using the Agent software but said it did not work since since it requires read 1 and read 2
illumina reads but we have nanopore reads.

Any suggestions?

Jackson

On Thu, Mar 26, 2020 at 12:33 PM ngs.support@agilent.com <ngs.support@agilent.com> wrote:

Hi Jackson,

Please see attached app note for using SureSelect probe on Nanopore sequencer.

Thanks,

Weiwei

From: Mandar Bedse (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>

Sent: Thursday, March 26, 2020 10:34 AM
Cc: SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com>; NGS.SUPPORT (Shared)
<ngs.support@agilent.com>; jleong@gigagen.com
Subject: RE: SureSelect library structure

jleong@gigagen.com, Mar 27, 1:55 AM IST:

Thanks,

Our bioinformatic person tried using the Agent software but said it did not work since since it requires read 1 and read 2
illumina reads but we have nanopore reads.

Any suggestions?

Jackson

Hi Jackson,

Please see attached app note for using SureSelect probe on Nanopore sequencer.

Thanks,

Weiwei

From: Mandar Bedse (Agilent Informatics Support) <informatics_support@cartagenia.zendesk.com>

Sent: Thursday, March 26, 2020 10:34 AM
Cc: SUPPORT,INFORMATICS (Shared) <informatics_support@agilent.com>; NGS.SUPPORT (Shared)
<ngs.support@agilent.com>; jleong@gigagen.com
Subject: RE: SureSelect library structure

NGS.SUPPORT (A-Santa Clara,exgen1), Mar 27, 1:03 AM IST:

Hi Jackson,

Please see attached app note for using SureSelect probe on Nanopore sequencer.

Thanks,

Weiwei

Attachment(s)
Sure Select+ Oxford Nanopore e.pdf

Mandar Bedse, Mar 26, 11:03 PM IST:

Hi NGS team,

Please help Jackson with his adapter experiment related question below

https://outlook.office.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAAAAB… 2/6
4/1/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook

Best Regards,
Mandar Bedse
Agilent Informatics Support

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jleong@gigagen.com, Mar 26, 11:00 PM IST:

Mandar,

Do you have ideas of prepping a sureselect for nanopore? For example, instead of adding the Illumina adapters, we add
the nanopore adapters and barcodes to be used for amplifying the enriched library?

Thanks,
Jackson

Mandar Bedse, Mar 26, 10:55 PM IST:

Hi Jackson,

Let us know if you need any further help.

Best Regards,
Mandar Bedse
Agilent Informatics Support

AUTO-NOTIFICATION: Please be advised that any forward/reply of this message (internal or

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Mandar Bedse, Mar 24, 2:22 AM IST:

Hi Jackson,

Greetings from informatics support.

You can use Trimmer for this purpose which is a command-line tool of Agilent. See page 4
from the below document.
https://www.agilent.com/cs/library/software/Public/AGeNT%20ReadMe.pdf

Download Agent tool using the link below:

https://www.agilent.com/en/download-agent-tool?
productURL=https%3A%2F%2Fwww.agilent.com%2Fen%2Fproduct%2Fnext-generation-
sequencing%2Fhybridization-based-next-generation-sequencing-ngs%2Fngs-
software%2Fagent-232879

https://outlook.office.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAAAAB… 3/6
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Regards,
Mandar Bedse

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NELSON,BETH (A-United States,ex1), Mar 24, 1:50 AM IST:

Further correspondence below:

Beth,

This is still being worked on from our bioinformatician and I will give you an update if more information is given to me. I
think she figured out she was looking at it in the incorrect direction.

Any advice on trimming the illumina adapters or using different adapters for sureselect would be helpful if anyone on the
informatics support team has any information on this.

Jackson

Best regards,

Beth Nelson

Genomics Applications Scientist – sequencing specialist

Diagnostics and Genomics Group

Agilent Technologies, Inc.

Tel: 1-800-227-9770 3, 4,4

ngs.support@agilent.com

NGS.SUPPORT (A-Santa Clara,exgen1), Mar 23, 11:30 PM IST:

Hello Jackson-

I have not received an email from you after our phone conversation Friday.

You inquired about seeing 14 bp instead of 10 bp for the molecular bar codes when modifying our SureSelect XT HS
protocol for Nanopore sequencing.

I have added our informatics support team to this email in the hope that you are able to share more details and they will
be able to advise you for trimming and analysis.

Best regards,

Beth Nelson

Genomics Applications Scientist – sequencing specialist

Diagnostics and Genomics Group

Agilent Technologies, Inc.

Tel: 1-800-227-9770 3, 4,4

ngs.support@agilent.com

From: NGS.SUPPORT (Shared)

Sent: Thursday, March 19, 2020 2:09 PM
https://outlook.office.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAAAAB… 4/6
4/1/2020 Mail - SUPPORT,INFORMATICS (Shared) - Outlook
To: 'jleong@gigagen.com' <jleong@gigagen.com>
Subject: SureSelect library structure

Hello Jackson-

Thank you for contacting Agilent Technical Support.

Please see the attachment to use as a quick reference foe the library structure of our various SureSelect library kits.

Best regards,

Beth Nelson

Genomics Applications Scientist – sequencing specialist

Diagnostics and Genomics Group

Agilent Technologies, Inc.

Tel: 1-800-227-9770 3, 4,4

ngs.support@agilent.com

NELSON,BETH (A-United States,ex1), Mar 23, 11:22 PM IST:

Hello Jackson-

I have not received an email from you after our phone conversation Friday.

You inquired about seeing 14 bp instead of 10 bp for the molecular bar codes when modifying our SureSelect XT HS
protocol for Nanopore sequencing.

I have added our informatics support team to this email in the hope that you are able to share more details and they will
be able to advise you for trimming and analysis.

Best regards,

Beth Nelson

Genomics Applications Scientist – sequencing specialist

Diagnostics and Genomics Group

Agilent Technologies, Inc.

Tel: 1-800-227-9770 3, 4,4

ngs.support@agilent.com

From: NGS.SUPPORT (Shared)

Sent: Thursday, March 19, 2020 2:09 PM
To: 'jleong@gigagen.com' <jleong@gigagen.com>
Subject: SureSelect library structure

Hello Jackson-

Thank you for contacting Agilent Technical Support.

Please see the attachment to use as a quick reference foe the library structure of our various SureSelect library kits.

Best regards,

Beth Nelson

Genomics Applications Scientist – sequencing specialist

Diagnostics and Genomics Group

Agilent Technologies, Inc.

Tel: 1-800-227-9770 3, 4,4

ngs.support@agilent.com
https://outlook.office.com/mail/informatics_support@agilent.com/AAMkAGZjYjEzMzczLWUwYjEtNGFlZi1hMjdiLTBjMGRiMWM4NDE3ZAAuAAAAAAB… 5/6
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