Import a BAM file into SMRT Link

Antony03 · 07-02-2019, 04:56 AM

Hello everyone,

I just sequenced bacterial genomes by PacBio Sequel. Compared to the RS II technology, I received a BAM file from the sequencing platform. I would like to import my sequencing data into SMRT Link, but I see that I need an XML file (the platform does not seem to be able to give me this file). Is there a way to generate this file or another way to integrate my data into SMRT Link?

Thank you

rhall · 08-30-2019, 01:13 PM

A service provider should be providing a xml file that can be used for import into SMRT Link.
You can generate a dataset xml using `dataset create` but it isn't ideal as you may be missing some required metadata.

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07-02-2019, 04:56 AM	#1
Antony03 Member Location: Canada, Quebec Join Date: Apr 2012 Posts: 53	Import a BAM file into SMRT Link Hello everyone, I just sequenced bacterial genomes by PacBio Sequel. Compared to the RS II technology, I received a BAM file from the sequencing platform. I would like to import my sequencing data into SMRT Link, but I see that I need an XML file (the platform does not seem to be able to give me this file). Is there a way to generate this file or another way to integrate my data into SMRT Link? Thank you

08-30-2019, 01:13 PM	#2
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 322	A service provider should be providing a xml file that can be used for import into SMRT Link. You can generate a dataset xml using `dataset create` but it isn't ideal as you may be missing some required metadata.