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Hello,
I'm working on 16S metabarcoding paired-end Illumina MiSeq data, in particular I would like to remove the primer sequences. I am very new in bioinformatics and command-line so I apologise i…
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I'm trying to merge two phyloseq objects (from 16S data produced using the same closed reference pipeline, just different runs) using merge_phyloseq. The problem is that the resulting merged object do…
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In my tests, the last condition of that function is never met (line 652):
```c++
int compare_amp(const void * a, const void * b)
{
const unsigned int * x = static_cast(a);
const unsigned int …
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Hello, I am losing a large portion of my reads at the merge and chimera removal steps. The primers have been removed. My reads are from the V3-V4 region. My quality profiles look good so I might no…
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this is my command:
`seqtab.nochimPerSimple Warning messages:
> 1: In doTryCatch(return(expr), name, parentenv, handler) :
> restarting interrupted promise evaluation
> 2: In doTryCatch(return(…
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@khdusenbury, I looked at the [JOSS manuscript submission instructions](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements), and I have the following suggestions to build on…
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Hi! I've been looking at the output from Swarm by tuning different parameters into it. I've tried with `-d 1`, `-d 2`, and `-d 3.` However, when I run it using `-d 0`, I get empty internal files, and …
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Hi there,
I am currently dealing with a dataset of 16S OTUs from sediment of two Antarctic cruises. I notice that in some of the phyloseq tutorials, the following is used:
```
dds1 = phyloseq_to_des…
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In the QIIME workflow, I am trying to replace the very slow and not appropriate vsearch classification of long-read metagenomics sequencing (ONT) by minimap2 which is very fast for this kind of reads.…
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Hello,
I would like to ask for some help regarding identification of chimera in a single sample. In this case, it was V3/V4 sequencing. I used MinFoldParentOverAbundance=16 and "consensus" method…
JoBrz updated
4 years ago