lotus2

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Trying to process ONT partial LSU amplicons

4

I'm trying to cluster with VSEARCH and assign taxonomy to a set of samples using partial LSU amplicons (in fasta format) PREVIOUSLY extracted from ONT long reads using ITSx. I...

SebaZambrano

LotuS2 Error: Missing LotuS_progout.log

3

Hello, I was trying to run the below command for analyzing full-length ITS sequences: ./lotus2 -i /my/PacBioDir/ -s configs/sdm_PacBio_ITS.txt -m PacBioDir/my_PacBio.map -o /my/PacBio/LotuS2 -p PacBio -id 0.97 -CL cdhit -refDB...

atfdh

reference DB when using RDPclassifier

1

Hi, If I run lotuS2 with `-taxAligner 0`, the option `-taxAligner` seems to be ignored. Am I right? From the logs, it appears that the RDP database was used: `[cmd]...

CFox-Lin

triming process and saving trimmed reads

1

Dear all, We are trying to se Lotus2, with dada2, to analyse some Illumina 16S data. We have two questions: - When using dada2 directly, one would typically have to...

ramiroricardo

save demultiplex

2

Hi, If I run lotus2 with `-saveDemultiplex 3` it results in an error. Can't say exactly what is happening. I don't find the log file where the error should be...

johnrandallia

-taxOnly seems to discard some sequences

2

Hello, I am running lotus2 only for taxonomy assignment of ITS1 sequences (so -taxOnly) (which is great! works super fast). I assumed that the output file would contain the same...

ingeborgklara

Errors with SDM

1

Hello, I am running Lotus2 on merged paired end illumina reads and am coming up with a weird issue. I am able to go through read filtering then I get...

thecrobe

Option to handle read-through into primer for its sequences

2

We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html Can lotus trim primers...

paulzierep

sdm dereplicated output file empty

8

Hi, I tried running lotus2 but got the following error: This is sdm (simple demultiplexer) 2.17 beta. Checking for switched pairs. Run with 12 cores.At lotus2/SRR13436190_1.fastq: Undecided fastq version.. sdm...

TJVUMC

Same ASV assigned to different taxonomy in two samples

1

Hi, Im looking to get consistent results per samples such that sample X in cohort A will have the same results as the same sample X in cohort B. I...

Amanda-Biocortex