Import a BAM file into SMRT Link

Question

[a.vincent.0312]

Hello,

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

[GenoMax]

I think you will have to ask your sequence provider to send you the XML file.

Answer 1

[sunilthorat]

I am using SMRT Link 6.0 for the first time. I already have Plant Genome RAW sequences data from PacBio RS II with files as under:

.adapters.fasta, .controls.fasta, .subreadset.xml, .sts.xml, .subreads.bam.pbi, scraps.bam.pbi, .subreads.fasta.gz, .subreads.bam and .sccraps.bam files

Now I want to import the .bam files and perform the SMRT analysis but I am unable to upload the .bam file into SMRT Link, Please help me.