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I have a data from 16S/18S/ITS Amplicon Sequencing. Can I use dada2 for analyzing such data? Should I divide them into 16S, 18S and ITS subsets as the reads have different lengths?
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Hi,
I found a typo in the output VCF that is causing errors when parsing. The AF parameter has NUMBER=1, so it must have exactly 1 entry, but with the recent update of adding af for all alternate all…
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Hi Ben,
Recently i used DADA2 on my 16s amplicon samples. As my samples had variable sequencing depth and quality, i transformed and rarefied my ASV counts to a uniform sequencing depth. Now, i …
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Dear community,
I am having memory issues while running the "Bioconductor workflow for microbiome data analysis: from raw reads to community analyses" and need some orientation. I am using this wor…
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I have been trying to assemble a 10Mb genome with uncorrected nanopore data (3-4 chromosomes expected). We have a lot of data, is that the reason Flye fails at the end?
[2019-06-22 11:00:05] INFO: …
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Dear Clair3 dev team,
## Background
I am using Clair3 for SNV/indel detection from ONT sequence data. The sequence data is from an amplicon sequencing experiment (high read coverage) of a mixed SA…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…
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Dear experts and colleagues,
I am doing 16S amplicon sequencing for the V3-V4 region. I am wondering whether I can directly use "silva_nr99_v138.1_train_set.fa.gz" for taxonomic assignment or if I …
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Hi, am running 16s Hifi demultiplexed analysis, after running the last line of code in this chunk:
meta_ana
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Hi Drs,
I tried to use this software to run learnErrors. I have been running for three or four days with no results, how can I solve it?
reads.in reads.out
Gr1m1-1_R1_00…