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I just read the Dada2 paper and worked through the tutorial. Very impressive work and software! I look forward to including Dada2 into the workflow for several of our current projects.
I apologiz…
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Dear all,
I am working with two ITS datasets (each with 96 samples sequenced in two MiSeq runs) from rhizosphere and bulk soil samples. These samples were PCR-amplified using 5.8S-Fun and ITS4-Fun…
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Hi, I did indexing for bovine genome reference UMD3.1, and am doing the further alignment.I have encountered Chromosomal sequence could not be extracted errors when processing trimmed WGBS FastQC data…
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We currently use bowtie2 to map reads to a large set of reference sequences. For most samples, it works well. However, we have had some problems with reference drift (#290), calling HCV subtypes (#436…
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Hello! I'm doing 16s amplicon sequencing on Illumina MiSeq 2x300 using 341F-806 primer set.
I've ran into a problem where we are losing over half our denoised reads at the merging step. The sequence…
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Hi there,
We've been analyzing a batch of 18S mock communities using DADA2. We put the mock communities together by mixing 22 unique, cloned, full-length 18S amplicons (Sanger sequenced before mix…
dcat4 updated
5 years ago
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I'm a new dada2 user and I've been struggling with 2 datasets 2x300 amplified using primers 27F and 519R. The samples are from microbiome of algal cultures.
The reverse reads are quite bad quality, b…
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Hello Pierre,
I have a conceptual problem. For a set of query sequences coming from metagenomic origin, I want to know the taxonomy. I have a reference tree with ~600 sequences. Should I:
- Pe…
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A small subset of sequences in CAR (and other AMR databases) have not been reverse-complemented in their FASTA representation. This is inconsistent with the other entries.
Some entries do revcom t…