Tag: DADA2

Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

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An error about using DADA2 in QIIME2 – Community Plugin Support

Hi everyone,I analyzed my pacbio data according to this PR, but an error was happened: Error in h(simpleError(msg, call)) : Error: invalid class “SRFilterResult” object: superclass “Mnumeric” no t defined in the environment of the object’s class stop Traceback (most recent call last): File “/home/xxx/miniconda3/envs/qiime2-2021.4/lib/python3.8/site- packages/q2_dada2/_denoise.py”, line 361, in denoise_ccs…

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cutadapt / trim-paired / option “front” and “adapter” – User Support

Hello, I have sequences in paired end that have both primers in R1 and R2 files.For exemple, a sequence in the forward ( R1 ) file :In bold the 2 primers : GTACACACCGCCCGTCGCTCCTACCGATACCGGGTGATCCGGTGAACCTTTTGGACCGTTTTTCGGAAAAATAAGTAAACCATATCACCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCAAGACCAAGTCTCTGCTACCGTACGTCTTCTTAATCTCGTATGCCGTCTTCTGCTTGAAAATTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG A sequence In the reverse ( R2 ) file: TGATCCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCTAGGTGATATGGTTTACTTATTTTTCCGAAAAACGGTCCAAAAGGTTCACCGGATCACCCGGTATCGGTAGGAGCGACGGGCGGTGTGTACTGTAGAACCATGTCGTCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAACGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG I wish to remove the primers to…

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qiime2-import data from non-working directory – User Support

Hello, qiime2 users community! I have the following set-up: a huge collection of .fastq files which I would like to process with the dada2 pipeline a remote cluster of servers with the separated storage where those files are stored, and the working machines for computing. Question: Is it possible to…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Which files from PacBio output files to use in downstream analysis in R

Which files from PacBio output files to use in downstream analysis in R 0 I just received Pacbio sequences of 16S gene from the core facility. After download, I got 5 files for each sample with following suffix: .ccs.bam longest.bam scraps.bam subreads.bam whitelist From readings, I believe that I should…

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How to map SILVA taxa names to NCBI IDs (in R)?

How to map SILVA taxa names to NCBI IDs (in R)? 0 Hi, How to map taxonomy assigned using SILVA database to NCBI ID (preferably in R)? I’m using R Dada2 and SILVA database to assign taxonomy: Bacteria > Firmicutes > Bacilli > Lactobacillales > Enterococcaceae > Enterococcus I need…

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