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Old 02-11-2014, 08:24 AM   #1
jbadalam
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Location: Saint Paul, MN

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Default PacBio internal control showing up in polished HGAP assembly

I noticed something odd when running two different HGAP assemblies. In both cases, the polished_assembly.fasta files contained a ~4kb contig with >3000x coverage. It matches the sequence of PacBio's 3-10kb SMRTbell internal control, and when I run resequencing or base modification pipelines it shows the control spike data. I just can't figure out why it's showing up in the final assembly.

This doesn't appear to be a huge issue, since I can just remove the contig from the fasta file. Just wondering if anyone else has encountered this.

The pipeline I used was HGAP.2 in SMRTanalysis 2.1.0.
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Old 02-11-2014, 09:03 AM   #2
rhall
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The internal control is not removed in the HGAP process, the expectation is that it results in a single contig for the control.
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Old 02-11-2014, 09:09 AM   #3
jbadalam
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Makes sense. Thanks for the rapid reply!
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