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Hi @benjjneb,
I've been processing some old amplicon sequencing sets with dada2 recently with no trouble (I'm a big fan) . However the last set of paired reads seems to have a mix of primer orienta…
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In the exercise, the code fails when executing:
```
primer_df, blat_df = AnoPrimer.designPrimers(
species='gambiae_sl',
assay_type='qPCR primers', # assay_type options are: 'qPCR pr…
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Hi everyone,
I encounter an unexpected behavior of `seqkit amplicon`: `seqkit amplicon -p` returns a different result than `seqkit amplicon -F -R`.
seq.fasta
```
>seq1
ATGCGCTATATATATTTT
>se…
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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-…
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Hello.
I'm checking the files for download and I see some file with name "refseq207nr_classifierpairA.qza", are this files for use with qiime2? Why are there classifierpairB and C?
What is the c…
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Create an option specific to light chains, this would call an LC_report.Rmd instead of a HC. Or the processing of LC is in the same file but there is a conditional argument somewhere to do that.
The…
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Hello all.
We have extracted DNA from tomato leaves and roots. The DNA was amplified using the 16S primers 515f/806r and ITS primers gITS7/ITS4 (ITS2 region). We used PNA clamps with the 16S PCRs to …
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computation with active SVD works like a charm
```
(qiime2-amplicon-2023.9) rs500-bcf-01 x86_64 ~/MicrobiomeAnalyses/Projects/Pandyra_CBP_Mb1-Cre>qiime gemelli tempted-factorize --i-table tempted_co…
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Using qiime2-amplicon-2024.2 with CLI
qc-rarefy errored on the first sample that is in the unrarefied and not in the rarefied dataset
Code:
```
qiime gemelli rpca \
--i-table ../data/core_d…
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We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html
Can …