-
Hi guys,
Thanks for developing this great suite of tools. I have a question regarding the applying UMI_tools extract to identify cell barcodes from what is essentially an amplicon sequencing ex…
-
Hey,
This seems like a very nice tool.
I wanted to use it for demultiplexing a paired-end MiSeq run (ITS2 amplicon sequencing) where we used custom 8-nt CDIs as i5 and i7 and an additional 4-nt ba…
-
### Is your feature related to a problem?
Most people doing environmental samples do amplicon sequencing for mixed communities so it would be convenient to have a solution for handling this kind of d…
-
**Describe the bug**
I am trying to align CRISPR-edited genomic amplicons to my amplicon reference template. When I align these amplicons to its reference using minimap2, I get 10,000+ reads aligning…
-
Hi,
I am having some troubles with some 16S V3-V4 region paired-end reads. It has been pooled in 4 libraries which I have received back demultiplexed into the pools containing my samples (about 30…
-
These SNPs look true on IGV. Why are they labelled as RefCall by Clair3? The AF values in the output VCF are around 0.5.
Another question: Clair3 is to find germline variants. However, my data is…
-
In the example you have the following:
```
gunzip -c reads.fastq.gz | chopper -q 10 -l 500 | gzip > filtered_reads.fastq.gz
```
Is this what you would recommend for the default settings? I'm…
-
I'm trying to run DADA2 via QIIME2 and noticing that it's very hands-on and not completely automated.
**Are there any reliable tools that can indicate where I should trim my forward and reverse rea…
-
The paper that describes the method mentions single-cell transcriptomics, CyTOF, and microbiome sequencing as applications. I have read the paper and description of the statistical model and I am appl…
-
Dear dada2 enthusiasts,
Upon analyzing my HTS (Illumina Miseq 2x300bp) data generated after amplification of the CO1 I3-M11 fragment (ca. 396 bp without primers) I am faced with doubts about the co…