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Forum: Metagenomics 04-18-2018, 11:47 AM
Replies: 13
Views: 7,672
Posted By pmiguel
Yes, we tried it, although not extensively. It...

Yes, we tried it, although not extensively. It worked, just no better than without denaturation.

Remember there is nothing to stop the denatured molecules from re-annealing--especially at the...
Forum: Metagenomics 04-18-2018, 07:45 AM
Replies: 13
Views: 7,672
Posted By pmiguel
Just keep in mind you would likely need to run...

Just keep in mind you would likely need to run the samples after heat denaturation/snap cooling on a denature chip -- eg, an RNA chip.

--
Phillip
Forum: Metagenomics 04-17-2018, 01:42 PM
Replies: 13
Views: 7,672
Posted By pmiguel
Mostly from amplicon libraries submitted by...

Mostly from amplicon libraries submitted by customer labs. I'm speculating that they are primers and primer-dimers. But who knows? We have seen them in some Nextera XT libraries. And to less extents...
Forum: Metagenomics 04-17-2018, 09:13 AM
Replies: 13
Views: 7,672
Posted By pmiguel
Those are just 16S sequences. Since FastQC only...

Those are just 16S sequences. Since FastQC only appears to be looking at the first 50 bases, I don't think it is a good assessment of the presence of primer dimers in your libraries. You could follow...
Forum: Metagenomics 04-16-2018, 05:50 AM
Replies: 13
Views: 7,672
Posted By pmiguel
The length of the reads in your .fastq file...

The length of the reads in your .fastq file likely does not include low-quality base clipping. The MiSeq will happily call bases on background noise. So the length of the reads is not diagnostic for...
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