-
I'm working with 16S amplicon sequences from rhizosphere soil and to process my data I'm using the DADA2 version 1.30.0 pipeline in R.
When calculating the error rate of my reverse sequences with t…
-
As stated in the title, I'm running into this issue and I'm not sure how to proceed or fix this?
> out head(out)
reads.in reads.out
SRR14825040_1.fastq.gz 644802 2219…
-
Hello, During the rule_reformat_filter_clusters step, only 36% of the clusters are being written, and I am not sure why. I understand this is happening in parse_clusters.py but have not been able to i…
-
Hi developers,
Recently, I used seqkit amplicon to extract the target sequence from the compressed FASTQ file by giving primer sequence. I downloaded the latest version (v2.7.0) and the previous ve…
-
Hi there, I have a problem about processing time series data using dada2 (groundwater). I took over a project that has been running already for 9 years and has been ongoing. My former colleague ran pr…
-
Dear @benjjneb, I ran DADA2 on my microbiome data and got an issue with taxonomic assignment.
I am working with synthetic microbial community so used customized database (full length 16S rRNA gene s…
-
I am trying to run 16S reads on dada2 but I can not get my reads to merge. I just get this message.
> mergers
-
OS Ubuntu 18.04 (within a docker container)
htslib v1.10.2 compiled from source (also when installed from the v0.7 apt package)
gcloud SDK v235.0.0-0 installed from apt package
We have a large wo…
-
I am running openPrimeR on a set of 65 sequences to develop primers for amplicon sequencing. I previously had the package up and running properly on a dummy dataset, but now that I'm running on my act…
-
Hello,
I am using Clair3 for variant calling on amplicon sequencing data. These reads were basecalled using Dorado (dna_r10.4.1_e8.2_400bps_sup@v4.3.0 model). For Clair3, I am using the r1041_e82_4…