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Unexpected amplicon sizes in MinION MK1D sequencing run (16S, 18S, 28S, ITS)
Hi everyone! We are using a MinION MK1D sequencer with its corresponding software for basecalling, and EPI2ME for data interpretation. We performed an... -
Sage Science Blue Pippin Supplies unavailable
Hi all,
We ordered cassettes for our Blue Pippin back in March and are still getting the run around from the company (https://sagescie... -
Use .fastq.gz instead of .fastq files in DADA2 pipeline
https://benjjneb.github.io/dada2/tutorial.html
The link above is the DADA2 pipeline in R that I've been using to analyse sequencing data (16S)... -
16S & 18S Deep Sequencing Request(s)
Hello,
We've done 16S/18S/ITS/amplicon sequencing for years, with good results - sometimes excellent (library dependent) - for both internal... -
SYBR-Gold for 16S library QC
Hi
I'm trying to prepare my first 16s library for ~100 samples and two variable regions, so exciting!!
I've read A Lot of... -
MiSeq run failed; low clustering, but good QC
Have a strange situation, our latest MiSeq run failed for 16S - from a protocol (EMP @ ArgonneNatLabs) that we use all the time.
The clustering... -
How to normalize/pool a 16S library when samples are highly variable concentrations??
Hi all,
I've been having this issue that has been plaguing my PhD. Some of my sequencing runs come back with terrible uneven read coverage....Last edited by samd; 03-21-2020, 09:36 AM. -
discrepancy in miseq runs due to sample prep protocol?
Hi all,
I have had an issue where my first ever Miseq run was great quality: 100k reads per sample with a nice distribution and then after... -
Taxonomy tree conflicts in Greengenes V 13.5
Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was... -
Taxonomy tree conflicts in Greengenes V 13.5
Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was... -
Target 16S V4 rRNA and ITS genes in one primer pool
The NEXTFLEX® 16S V4 and 18S ITS Amplicon-Seq kit enables highly efficient, sensitive and specific identification of bacteria, fungus, and other microorganisms... -
Is amplicon/16S sequencing a thing of the past?
I've been tossing up posting this for a little while, but decided, why not!
I work in a facility where we do 16S and shotgun metagenomics... -
FastQC results for 16s reads
Hi
I have some FastQC results I have generated from Illumina 16s sequences. I have attached an example of the results for one of the demultiplexed... -
MiSeq v3 (2X300PE) 16S sequencing, no values for clusters PF
We recently have problems with 16S runs. We have been following the illumina protocol for v3-v4 regions, but have difficulties to get the optimum cluster... -
Qiime vs illumina basespace 16s pipeline, Which is better?
Hello everyone, we currently handle a 16 project which analyzed by QIime and illumina basespace 16s app. The results are quite different. I googled and...
