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Currently we generate the mapping files for an amplicon run with the `amplicon-pooling.ipynb` notebook, however this should be changed to work the same was as with metagenomics runs. Namely using the …
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HI:
I use the jacusa2 to run my amplicon data, but the result lost the last position of the ref, that is, if my ref is 182bp long, the jacusa2 result only print the 1-181bp. The parameters I used…
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I'm using geminimulti and pisces on some targeted amplicon sequencing, but each run might contain a different mix of amplicons located around the genome so I can't easily use the chromosomes option to…
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I am trying to understand how to adjust -k since it seems to impact the results dramatically.
For example with primers of length 25 and a -k of 15 I get no amplicons.
I think this is the same as cha…
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JSON should be identical to that from 0.3.7 but
a) with line breaks, eg indent =2,
b) with an additional summary block, containing:
“Summary”: {
“command”: “viridian run_one_sample fq1 fq2”…
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Hi Author(s),
I think it is super cool that you've implemented this dynamic strategy!
We where trying to normalize some amplicons on a given chromosome, so we made sequences that where unique to…
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Hey,
thanks for the great simulation tool! We simulated reads using this command:
```bash
conda activate SWAMPy
python simulate_metagenome.py \
--genomes_file ../example/viralref.fasta \…
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**Describe the bug**
I encounter tow type of errors while using CRISPResso2. The ERRORs are **quantification window ERROR** and **invalid characters ERROR**
I upload all the fastq.gz file [here]…
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accumulate papers describing oligotypes and amplicon sequences and exact sequence variants
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Hi all,
The read_clustering step failed for whole operons (16S-ITS-23S, ~4.1k mean read length).
The whole nextflow pipeline ran through without errors (on a Mac M1) with test fastq files `mock4…