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Heya,
I have two runs (rep1, rep2) of 16S amplicon sequencing for 40 samples. The samples in 'rep1' are named like '1062-1-sampleNo1.R1.fastq' through '1062-1-sampleNo40.R1.fastq' and '1062-1-sample…
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In my collaborations, I often encounter situations where PhD candidates are volunteered by their PI's to also handle amplicon analysis, but are total microbiome newbies. Situations might be complicate…
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Dear, @benjjneb !
A company performed a metabarcode sequencing (V3-V4 regions of the 16S rRNA gene) and sent to me the paired reads, already trimmed. The reads F and R came with the average lengths…
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## Template Fixes:
## Specification Changes:
| Field | Change |
| --- | --- |
| `sequencing_assay_type` | New field |
| `host (common name)` | New picklist IDs |
| `host (scientific name)`…
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Hi,
I've been using minimap2 for quite some time now, however I recently ran into a problem with it. We used Oxford Nanopore to sequence a PCR amplicon, which has a polyA-region, followed by ~30 bp…
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Sorry for disturbance, may I ask if the meaning of exact match is 100% identical between ref seq and reads?
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**Describe the bug**
There is no png or pdf file generated for the allele frequency table. I do get the .zip archive containing the allele frequency table in .txt format, but no graphic. Usually cris…
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Hi Ben,
I am big fan of DADA2 for analysing 16S data. I recently worked with AmpliSeq data generated on Illumina with paired-end. In nutshell, multiple targets (AMR genes) (>800) were amplified and…
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Hi, I am looking at some data from the 2 x 150 bp V4 region, and when I look at the quality plot, we see a drop in the middle of the read for both forward and reverse. Furthermore, we see that many of…
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When I run WhatsHap in vcf + bam (Illumina amplicon sequencing) mode (no pedigree) for data that looks like this:
![image](https://github.com/whatshap/whatshap/assets/1266815/e01b1361-de00-4ed5-ba29-…